X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=sql-classes.lisp;h=d086fd4969689c1ecf9424ef17616be5314510e1;hp=b6abb486af5d54d9da189699f14d2d8ed4d21bf8;hb=HEAD;hpb=3846affd569e67e66a84465c070375c47c417265 diff --git a/sql-classes.lisp b/sql-classes.lisp index b6abb48..d086fd4 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -2,476 +2,968 @@ ;;;; ************************************************************************* ;;;; FILE IDENTIFICATION ;;;; -;;;; Name: sql-classes.lisp -;;;; Purpose: Routines for reading UMLS objects from SQL database -;;;; Author: Kevin M. Rosenberg -;;;; Date Started: Apr 2000 -;;;; -;;;; $Id: sql-classes.lisp,v 1.55 2003/05/03 22:45:23 kevin Exp $ +;;;; Name: sql-classes.lisp +;;;; Purpose: Routines for reading UMLS objects from SQL database +;;;; Author: Kevin M. Rosenberg +;;;; Created: Apr 2000 ;;;; ;;;; This file, part of UMLisp, is -;;;; Copyright (c) 2000-2002 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. ;;;; ************************************************************************* -(in-package :umlisp) -(declaim (optimize (compilation-speed 0) (debug 3))) +(in-package #:umlisp) (defvar *current-srl* nil) (defun current-srl () *current-srl*) -(defun current-srl! (srl) +(defun set-current-srl (srl) (setq *current-srl* srl)) -;; only WHERE-VALUE and SRL are evaluated -(defmacro with-umlisp-query ((table fields srl where-name where-value - &key (lrl "KCUILRL") distinct single - order like) - &body body) - (let ((value (gensym))) - (if single - `(let ((,value where-value)) - (when ,value - (let ((tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value - :lrl ,lrl :single ,single - :distinct ,distinct :order ,order - :like ,like)))) - (when tuple - (destructuring-bind ,fields tuple - ,@body))))) - `(let ((,value where-value)) - (when ,value - (loop for tuple in - (umlisp-query ,table ,fields ,srl ,where-name ,value - :lrl ,lrl :single ,single :distinct ,distinct - :order ,order :like ,like) - collect (destructuring-bind ,fields tuple - ,@body))))))) - -(defmacro umlisp-query (table fields srl where-name where-value - &key (lrl "KCUILRL") single distinct order like) - "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-macro ,table ,fields ,srl ,where-name ,where-value - :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like))) - - -(defmacro query-string-macro (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~)~^,~}" order) "")) - (%%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 - `((if (numberp ,where-value) - (write-to-string ,where-value) - (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 (table fields &optional srl where-name where-value - &key (lrl "KCUILRL") single distinct order like) +(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 " "") (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-"))) + `(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) + (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)" + (if distinct "DISTINCT " "") (sqlname fields) table) + (if where-name (format nil " WHERE ~:@(~A~)" (sqlname where-name)) "") (if where-name (format nil - (if (stringp where-value) - (if like - " where ~A like '%~A%'" - " where ~A='~A'") - " where ~A=~A") - where-name where-value) + (typecase where-value + (number "='~D'") + (null " IS NULL") + (t + (if like " LIKE '%~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" ""))) - -(defun find-ucon-cui (cui &key (srl *current-srl*)) - "Find ucon for a cui" - (with-umlisp-query (mrcon (kpfstr kcuilrl) srl cui (parse-cui cui) :single t) - (make-instance 'ucon :cui (parse-cui cui) - :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) - -(defun find-ucon-cui-old (cui &key (srl *current-srl*)) - "Find ucon for a cui" - (when (stringp cui) (setq cui (parse-cui cui))) + (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 + 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 + :filter ,filter :limit ,limit))) + +(defmacro umlisp-query-eval (table fields srl where-name where-value + &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 + :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) + filter limit) + &body body) + (let ((value (gensym)) + (r (gensym))) + (if single + (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 :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)))))) + +(defmacro collect-umlisp-query-eval ((table fields srl where-name where-value + &key (lrl "KCUILRL") distinct single + order like filter limit) + &body body) + (let ((value (gensym)) + (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 + :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 + :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 + :limit ,limit) + collect (destructuring-bind ,eval-fields tuple ,@body)))))) + +;;; +;;; Read from SQL database + +(defmacro ensure-cui-integer (cui) + `(if (stringp ,cui) + (setq ,cui (parse-cui ,cui)) + ,cui)) + +(defmacro ensure-lui-integer (lui) + `(if (stringp ,lui) + (setq ,lui (parse-lui ,lui)) + ,lui)) + +(defmacro ensure-sui-integer (sui) + `(if (stringp ,sui) + (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)) + ,tui)) + +(defmacro ensure-eui-integer (eui) + `(if (stringp ,eui) + (setq ,eui (parse-eui ,eui)) + ,eui)) + +(defun make-ucon-cui (cui) + (ensure-cui-integer cui) (when cui - (let ((ls (format nil "select KPFSTR,KCUILRL from MRCON where CUI=~d" cui))) - (when srl - (string-append ls (format nil " and KCUILRL <= ~d" srl))) - (string-append ls " limit 1") - (let ((tuple (car (mutex-sql-query ls)))) - (destructuring-bind (kpfstr kcuilrl) tuple - (make-instance 'ucon :cui cui :pfstr kpfstr - :lrl (ensure-integer kcuilrl))))))) - -(defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*)) - "Find ucon for a cui" - (with-umlisp-query (mrcon (kcuilrl) srl cui (parse-cui cui) :single t) - (make-instance 'ucon :cui (parse-cui cui) - :lrl (ensure-integer kcuilrl) - :pfstr nil))) + (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)) + + (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) + (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" - (with-umlisp-query (mrcon (kpfstr) srl cui (parse-cui cui) :single t) - kpfstr)) + (ensure-cui-integer cui) + (or + (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" - (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui (parse-lui lui) :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (ensure-lui-integer lui) + (unless lui (return-from find-ucon-lui nil)) + (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" - (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl sui (parse-sui sui) :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (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)))) + +(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)))) + +(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-cuisui (cui sui &key (srl *current-srl*)) +(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) - (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl kcuisui - (make-cuisui (parse-cui cui) (parse-sui sui))) - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr kpfstr - :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" - (with-umlisp-query (mrcon (cui kpfstr kcuilrl) srl str str :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl)))) (defun find-ucon-all (&key (srl *current-srl*)) "Return list of all ucon's" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query 'list - #'(lambda (cui pfstr cuilrl) - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl))) - (query-string 'mrcon '(cui kpfstr kcuilrl) srl nil nil - :order (cui asc) :distinct t) + #'(lambda (tuple) + (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) :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) + (make-instance 'ucon :cui (ensure-integer cui) + :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)) + (defun map-ucon-all (fn &key (srl *current-srl*)) "Map a function over all ucon's" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query nil - #'(lambda (cui pfstr cuilrl) - (funcall fn - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl)))) - (query-string 'mrcon '(cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t) + #'(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))))) + (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc) + :distinct t) :database db))) (defun find-udef-cui (cui &key (srl *current-srl*)) "Return a list of udefs for cui" - (with-umlisp-query (mrdef (sab def) srl cui (parse-cui cui) :lrl "KSRL") - (make-instance 'udef :sab sab :def def))) + (ensure-cui-integer cui) + (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) + "Return list of abbreviation documentation for a key" + (collect-umlisp-query (mrdoc (value type expl) nil dockey key) + (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 :dockey dockey :dvalue value :dtype type :expl expl))) + +(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 :dockey dockey :dvalue value :dtype type :expl expl))) (defun find-usty-cui (cui &key (srl *current-srl*)) "Return a list of usty for cui" - (with-umlisp-query (mrsty (tui sty) srl cui (parse-cui cui) :lrl "KLRL") + (ensure-cui-integer cui) + (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL") (make-instance 'usty :tui (ensure-integer tui) :sty sty))) (defun find-usty-word (word &key (srl *current-srl*)) "Return a list of usty that match word" - (with-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t :distinct t) + (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t + :distinct t) (make-instance 'usty :tui (ensure-integer tui) :sty sty))) -(defun find-urel-cui (cui &key (srl *current-srl*)) +(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" :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 (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" - (with-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1 (parse-cui cui) :lrl "KSRL") - (make-instance 'urel :cui1 (parse-cui cui) :rel rel :cui2 (ensure-integer cui2) :rela rela - :sab sab :sl sl :mg mg :pfstr2 kpfstr2))) + (ensure-cui-integer cui) + (collect-umlisp-query (mrrel (cui2) srl cui1 + cui :lrl "KSRL") + cui2)) (defun find-urel-cui2 (cui2 &key (srl *current-srl*)) "Return a list of urel for cui2" - (with-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2 (parse-cui cui2) :lrl "KSRL") - (make-instance 'urel :cui2 (parse-cui cui2) :rel rel :cui1 (ensure-integer cui1) :rela rela - :sab sab :sl sl :mg mg :pfstr2 kpfstr2))) + (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 (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)))) (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*)) - (mapcar - #'(lambda (cui) (find-ucon-cui cui :srl srl)) - (remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl 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))) -(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" - (with-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1 (parse-cui cui) - :lrl "KSRL" :order (cof asc)) + (ensure-cui-integer cui) + (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1 + cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) - (when (zerop cui2) (setq cui2 nil)) - (make-instance 'ucoc :cui1 (parse-cui cui) :cui2 (ensure-integer cui2) :soc soc :cot cot - :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2))) + (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)))) -(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" - (with-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2 (parse-cui cui2) - :lrl "KSRL" :order (cof asc)) - (setq cui2 (ensure-integer cui2)) + (ensure-cui-integer cui2) + (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2 + cui2 :lrl klrl :order (cof asc)) (when (zerop cui2) (setq cui2 nil)) - (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 (parse-cui cui2) :soc soc :cot cot - :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2))) + (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)))) -(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" - (mapcar + (ensure-cui-integer cui2) + (mapcar #'(lambda (cui) (find-ucon-cui cui :srl srl)) (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl))))) -(defun find-ulo-cui (cui &key (srl *current-srl*)) - "Return a list of ulo for cui" - (with-umlisp-query (mrlo (isn fr un sui sna soui) srl cui (parse-cui cui) :lrl "KLRL") - (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un :sui (ensure-integer sui) :sna sna - :soui soui))) - -(defgeneric suistr (lo)) -(defmethod suistr ((lo ulo)) - "Return the string for a ulo object" - (find-string-sui (sui lo))) - -(defun find-uatx-cui (cui &key (srl *current-srl*)) - "Return a list of uatx for cui" - (with-umlisp-query (mratx (sab rel atx) srl cui (parse-cui cui) :lrl ksrl) - (make-instance 'uatx :sab sab :rel rel :atx atx))) - (defun find-uterm-cui (cui &key (srl *current-srl*)) "Return a list of uterm for cui" - (with-umlisp-query (mrcon (lui lat ts kluilrl) srl cui (parse-cui cui) :lrl kluilrl - :distinct t) - (make-instance 'uterm :lui (ensure-integer lui) :cui (parse-cui cui) - :lat lat :ts ts :lrl (ensure-integer kluilrl)))) + (ensure-cui-integer cui) + (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui + :lrl kluilrl :distinct t) + (make-instance 'uterm :lui (ensure-integer lui) :cui cui + :lat lat :ts ts :lrl (ensure-integer kluilrl)))) (defun find-uterm-lui (lui &key (srl *current-srl*)) "Return a list of uterm for lui" - (with-umlisp-query (mrcon (cui lat ts kluilrl) srl lui (parse-lui lui) - :lrl kluilrl :distinct t) - (make-instance 'uterm :cui (ensure-integer cui) :lui (parse-lui lui) - :lat lat :ts ts :lrl (ensure-integer kluilrl)))) + (ensure-lui-integer lui) + (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui + :lrl kluilrl :distinct t) + (make-instance 'uterm :cui (ensure-integer cui) :lui lui + :lat lat :ts ts :lrl (ensure-integer kluilrl)))) (defun find-uterm-cuilui (cui lui &key (srl *current-srl*)) "Return single uterm for cui/lui" - (with-umlisp-query (mrcon (lat ts kluilrl) srl kcuilui - (make-cuilui (parse-cui cui) (parse-lui lui)) - :lrl kluilrl :single t) - (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts :lrl (ensure-integer kluilrl)))) + (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-instance 'uterm :cui cui :lui lui :lat lat :ts ts + :lrl (ensure-integer kluilrl)))) (defun find-ustr-cuilui (cui lui &key (srl *current-srl*)) "Return a list of ustr for cui/lui" - (with-umlisp-query (mrcon (sui stt str lrl) srl kcuilui (make-cuilui cui lui) :lrl lrl) - (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui - :cuisui (make-cuisui cui sui) :stt stt :str str - :lrl (ensure-integer lrl)))) + (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 :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" - (with-umlisp-query (mrcon (lui stt str lrl) srl kcuisui (make-cuisui cui sui) :lrl lrl :single t) - (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui) - :lui (ensure-integer lui) :stt stt :str str :lrl (ensure-integer lrl)))) + (ensure-cui-integer cui) + (ensure-sui-integer sui) + (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" - (with-umlisp-query (mrcon (cui lui stt str lrl) srl sui (parse-sui sui) :lrl lrl) + (ensure-sui-integer sui) + (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui + :lrl ksuilrl :distinct t) (make-instance 'ustr :sui sui :cui cui :stt stt :str str - :cuisui (make-cuisui (ensure-integer cui) (parse-sui sui)) - :lui (ensure-integer lui) - :lrl (ensure-integer lrl)))) - + :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" - (with-umlisp-query (mrso (kcuisui) srl sab sab :lrl srl) + (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" (with-sql-connection (db) - (clsql:map-query + (clsql:map-query 'list - #'(lambda (cui lui sui stt lrl pfstr) - (setq cui (ensure-integer cui)) - (setq lui (ensure-integer lui)) - (setq sui (ensure-integer sui)) - (setq lrl (ensure-integer lrl)) - (make-instance 'ustr :cui cui - :lui lui - :sui sui - :cuisui (make-cuisui cui sui) - :stt stt - :lrl lrl - :str pfstr)) - (query-string 'mrcon '(cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl :distinct t - :order (sui asc)) + #'(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)))) + (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl + :distinct t + :order (sui asc)) :database db))) (defun find-string-sui (sui &key (srl *current-srl*)) "Return the string associated with sui" - (with-umlisp-query (mrcon (str) srl sui sui :lrl lrl :single t) + (ensure-sui-integer sui) + (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t) str)) (defun find-uso-cuisui (cui sui &key (srl *current-srl*)) - (with-umlisp-query (mrso (sab code srl tty) srl kcuisui (make-cuisui cui sui) :lrl srl) - (make-instance 'uso :sab sab :code code :srl srl :tty tty))) - -(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*)) - (with-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc) srl kcuisui - (make-cuisui cui sui) :lrl ksrl) - (make-instance 'ucxt :sab sab :code code - :cxn (ensure-integer cxn) - :cxl cxl :cxs cxs :hcd hcd :rela rela :xc xc - :rnk (ensure-integer rnk) - :cui2 (ensure-integer cui2)))) - -(defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*)) - (let ((ls (format nil "select CODE,ATN,SAB,ATV from MRSAT where "))) + (ensure-sui-integer sui) + (ensure-cui-integer cui) + (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 :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 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 :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 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 :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) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + +(defun find-uhier-all (&key (srl *current-srl*)) + (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf) + srl nil nil :lrl ksrl) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + +(defun find-usat-ui (cui &optional lui 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 (format nil "KCUISUI=~d" (make-cuisui cui sui)))) - (lui (string-append ls (format nil "KCUILUI=~d and sui=0" (make-cuilui cui lui)))) - (t (string-append ls (format nil "cui=~d and lui=0 and sui=0" cui)))) + (sui (string-append ls "KCUISUI='" + (integer-string (make-cuisui cui sui) 14) + "'")) + (lui (string-append ls "KCUILUI='" + (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'"))) (when srl - (string-append ls (format nil " and KSRL <= ~d" srl))) - (loop for tuple in (mutex-sql-query ls) collect - (destructuring-bind (code atn sab atv) tuple - (make-instance 'usat :code code :atn atn :sab sab :atv atv))))) + (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))))) (defun find-usty-tui (tui) "Find usty for tui" - (with-umlisp-query (mrsty (sty) nil tui (parse-tui tui) :single t) - (make-instance 'usty :tui (parse-tui tui) :sty sty))) + (ensure-tui-integer tui) + (collect-umlisp-query (mrsty (sty) nil tui tui :single t) + (make-instance 'usty :tui tui :sty sty))) (defun find-usty-sty (sty) "Find usty for a sty" - (with-umlisp-query (mrsty (tui) nil sty sty :single t) + (collect-umlisp-query (mrsty (tui) nil sty sty :single t) (make-instance 'usty :tui (ensure-integer tui) :sty sty))) (defun find-usty-all () "Return list of usty's for all semantic types" - (with-umlisp-query (mrsty (tui) nil nil nil :distinct t) + (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t) (find-usty-tui tui))) (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) + (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 &key current) "Find usab for a key" - (with-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) nil nil nil) - (make-instance 'usab :vcui (ensure-integer vcui) - :rcui (ensure-integer rcui) - :vsab vsab :rsab rsab :son son :sf sf :sver sver :mstart mstart - :mend mend :imeta imeta :rmeta rmeta :slc slc :scc scc - :srl (ensure-integer srl) - :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) - :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc - :curver curver :sabin sabin))) - -(defun find-usab-by-key (key-name key) - "Find usab for a key" - (with-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) nil key-name key :single t) - (make-instance 'usab :vcui (ensure-integer vcui) - :rcui (ensure-integer rcui) - :vsab vsab :rsab rsab :son son :sf sf :sver sver :mstart mstart - :mend mend :imeta imeta :rmeta rmeta :slc slc :scc scc - :srl (ensure-integer srl) - :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) - :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc - :curver curver :sabin sabin))) - -(defun find-usab-rsab (rsab) + (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 + :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 &key (current t)) "Find usab for rsab" - (find-usab-by-key "RSAB" 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)) + (find-usab-by-key 'vsab vsab)) (defun find-cui-max () (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON")))) +(defun find-umap-cui (cui) + (ensure-cui-integer cui) + (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr + fromtype fromrule fromres rel rela toid tosid + toexpr totype torule tores maprule maptype + mapatn mapatv cvf) + nil mapsetcui cui) + (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid + :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid + :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres + :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype + :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn + :mapatv mapatv :cvf cvf))) + +(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*)) "Find list of ucon for tui" - (with-umlisp-query (mrsty (cui) srl tui (parse-tui tui) :lrl klrl - :order (cui asc)) + (ensure-tui-integer tui) + (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc)) (find-ucon-cui (ensure-integer cui) :srl srl))) - -(defun find-ucon-word (word &key (srl *current-srl*) (like nil)) - "Return list of ucons that match word. Optionally, use SQL's LIKE syntax" - (with-umlisp-query (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" - (with-umlisp-query (mrxnw_eng (cui) srl nwd word :like like :distinct t - :lrl klrl :order (cui asc)) + (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t + :lrl 'klrl :order '(cui asc)) (find-ucon-cui cui :srl srl))) -(defun find-ustr-word (word &key (srl *current-srl*)) - "Return list of ustrs that match word" - (with-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-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)) + +(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)) + +(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)) + +(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" - (with-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)) + (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)) + (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)) + (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 (kcuisui) srl wd word :lrl klrl + :order (cui asc sui asc)) + (find-ustr-cuisui kcuisui :srl srl))) ;; Special tables (defun find-usrl-all () - (with-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc)) + (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc)) (make-instance 'usrl :sab sab :srl (ensure-integer srl)))) ;;; Multiword lookup and score functions -(defun find-ucon-multiword (str &key (srl *current-srl*)) - "Return sorted list of ucon's that match a multiword string" - (let* ((words (delimited-string-to-list str #\space)) - (ucons '())) - (dolist (word words) - (setq ucons (append ucons (find-ucon-word word :srl srl)))) - (sort-score-ucon-str str (delete-duplicates ucons :test #'eql :key #'cui)))) - -(defun find-ustr-multiword (str &key (srl *current-srl*)) - "Return sorted list of ustr's that match a multiword string" - (let* ((words (delimited-string-to-list str #\space)) - (ustrs '())) - (dolist (word words) - (setq ustrs (append ustrs (find-ustr-word word :srl srl)))) - (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'cui)))) - -(defun sort-score-ucon-str (str ucons) +(defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl + only-exact-if-match limit &key extra-lookup-args) + (let ((uobjs '())) + (dolist (word (delimited-string-to-list str #\space)) + (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)))) + (let ((len (length sorted))) + (cond + ((zerop len) + (return-from find-uobj-multiword nil)) + ((and only-exact-if-match (multiword-match str (pfstr (first sorted)))) + (first sorted)) + (limit + (if (and (plusp limit) (> len limit)) + (subseq sorted 0 limit) + limit)) + (t + sorted)))))) + +(defun find-ucon-multiword (str &key (srl *current-srl*) + (only-exact-if-match t) + limit + sab) + (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str + #'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) + limit) + (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str + #'lui srl only-exact-if-match limit)) + +(defun find-ustr-multiword (str &key (srl *current-srl*) + (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 + :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" - (sort-score-umlsclass-str ucons str #'pfstr)) + (sort-score-umlsclass-str uobjs str #'pfstr)) (defun sort-score-ustr-str (str ustrs) "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr" @@ -481,139 +973,171 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Sort a list of objects based on scoring to a string" (let ((scored '())) (dolist (obj objs) - (push - (list obj - (score-multiword-match str (funcall lookup-func obj))) + (push (list obj (score-multiword-match str (funcall lookup-func obj))) scored)) (mapcar #'car (sort scored #'> :key #'cadr)))) -(defun score-multiword-match (s1 s2) - "Score a match between two strings with s1 being reference string" - (let* ((word-list-1 (delimited-string-to-list s1 #\space)) - (word-list-2 (delimited-string-to-list s2 #\space)) - (n1 (length word-list-1)) - (n2 (length word-list-2)) - (unmatched n1) - (score 0) - (nlong 0) - (nshort 0) - short-list long-list) - (declare (fixnum n1 n2 nshort nlong score unmatched)) - (if (> n1 n2) - (progn - (setq nlong n1) - (setq nshort n2) - (setq long-list word-list-1) - (setq short-list word-list-2)) - (progn - (setq nlong n2) - (setq nshort n1) - (setq long-list word-list-2) - (setq short-list word-list-1))) - (decf score (- nlong nshort)) ;; reduce score for extra words - (dotimes (iword nshort) - (declare (fixnum iword)) - (kmrcl:aif (position (nth iword short-list) long-list :test #'string-equal) - (progn - (incf score (- 10 (abs (- kmrcl::it iword)))) - (decf unmatched)))) - (decf score (* 2 unmatched)) - score)) - ;;; LEX SQL functions (defun find-lexterm-eui (eui) - (with-umlisp-query (lrwd (wrd) nil eui eui :single t) + (ensure-eui-integer eui) + (collect-umlisp-query (lrwd (wrd) nil eui eui :single t) (make-instance 'lexterm :eui eui :wrd wrd))) (defun find-lexterm-word (wrd) - (with-umlisp-query (lrwd (eui) nil wrd 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 (defun find-labr-eui (eui) - (with-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui) + (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) - (with-umlisp-query (labr (eui abr eui2 bas2) nil 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) - (with-umlisp-query (lragr (str sca agr cit bas) nil 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) - (with-umlisp-query (lrcmp (bas sca com) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrcmp (bas sca com) nil eui eui) (make-instance 'lcmp :eui eui :bas bas :sca sca :com com))) (defun find-lmod-eui (eui) - (with-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui) (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea))) (defun find-lnom-eui (eui) - (with-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui) + (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) - (with-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil 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) - (with-umlisp-query (lrprp (bas str sca fea) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui) (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea))) (defun find-lspl-eui (eui) - (with-umlisp-query (lrspl (spv bas) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrspl (spv bas) nil eui eui) (make-instance 'lspl :eui eui :spv spv :bas bas))) (defun find-ltrm-eui (eui) - (with-umlisp-query (lrtrm (bas gen) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrtrm (bas gen) nil eui eui) (make-instance 'ltrm :eui eui :bas bas :gen gen))) (defun find-ltyp-eui (eui) - (with-umlisp-query (lrtyp (bas sca typ) nil eui eui) + (ensure-eui-integer eui) + (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui) (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ))) (defun find-lwd-wrd (wrd) - (make-instance 'lwd :wrd - :euilist (with-umlisp-query (lrwd (eui) nil wrd wrd) - (ensure-integer eui)))) + (make-instance 'lwd :wrd wrd + :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd) + (ensure-integer eui)))) ;;; Semantic Network SQL access functions (defun find-sdef-ui (ui) - (with-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin) - nil ui ui :single t) + (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin) + 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) - (with-umlisp-query (srstre1 (ui2 ui3) nil 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) - (with-umlisp-query (srstre1 (ui ui3) nil 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) - (with-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl) + (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl) (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls))) (defun find-sstre2-sty (sty) - (with-umlisp-query (srstre2 (rl sty2) nil sty sty) + (collect-umlisp-query (srstre2 (rl sty2) nil sty sty) (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2))) (defun find-sstr-styrl (styrl) - (with-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl) + (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl) (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls))) + + +;;; ************************** +;;; Local Classes +;;; ************************** + + +(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)))) + ((null srl-control) + (ensure-integer + (caar (sql-query (format nil "select count(~a) from ~a" + count-variable table ) + conn)))) + (t + (error "Unknown srl-control") + 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)) + +(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))) + (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))))) + +(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-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-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))))