;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: sql-classes.lisp
-;;;; Purpose: Routines for reading UMLS objects from SQL database
-;;;; Programmer: Kevin M. Rosenberg
-;;;; Date Started: Apr 2000
+;;;; Name: sql-classes.lisp
+;;;; Purpose: Routines for reading UMLS objects from SQL database
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
;;;;
-;;;; $Id: sql-classes.lisp,v 1.17 2003/05/02 21:24:19 kevin Exp $
+;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2006 by Kevin M. Rosenberg, M.D.
;;;;
;;;; UMLisp users are granted the rights to distribute and use this software
;;;; as governed by the terms of the GNU General Public License.
;;;; *************************************************************************
-(in-package :umlisp)
-(declaim (optimize (compilation-speed 0) (debug 3)))
+(in-package #:umlisp)
(defvar *current-srl* nil)
(defun current-srl! (srl)
(setq *current-srl* srl))
-;;; Object lookups
-
-;;; Lookup functions for uterms,ustr in ucons
-
-(defun find-uterm-in-ucon (ucon lui)
- (find lui (s#term ucon) :key #'lui :test 'equal))
-
-(defun find-ustr-in-uterm (uterm sui)
- (find sui (s#str uterm) :key #'sui :test 'equal))
-
-(defun find-ustr-in-ucon (ucon sui)
- (let ((found-ustr nil))
- (dolist (uterm (s#term ucon))
- (unless found-ustr
- (dolist (ustr (s#str uterm))
- (unless found-ustr
- (when (string-equal sui (sui ustr))
- (setq found-ustr ustr))))))
- found-ustr))
-
-(defmacro with-umlisp-query ((table fields srl where-name where-value
- &key (lrlname "KCUILRL") distinct single terminal like)
- &body body)
- (let ((query (gensym)))
- `(unless (and ,where-name (not ,where-value))
- (let ((,query (umlisp-query ,table ,fields ,srl ,where-name ,where-value
- :lrlname ,lrlname :single ,single :distinct ,distinct
- :terminal ,terminal :like ,like)))
- (if ,single
- (let ((tuple (car ,query)))
- (when tuple
- ,@body))
- (loop
- for tuple in ,query
- collect
- ,@body))))))
-
-(defun umlisp-query (table fields srl where-name where-value
- &key (lrlname "KCUILRL") single distinct terminal like)
+(defmacro query-string (table fields &optional srl where-name where-value
+ &key (lrl "KCUILRL") single distinct order like)
+ (let* ((%%fields (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
+ (if distinct "distinct " "") fields table))
+ (%%order (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}"
+ 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
+ `((typecase ,where-value
+ #+ignore
+ (fixnum
+ (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
+ (number
+ (concatenate 'string "='" (write-to-string ,where-value) "'"))
+ (null
+ " is null")
+ (t
+ (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
+ (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
+ ,@(when %%order (list %%order))
+ ,@(when single (list " limit 1")))))
+
+(defun query-string-eval (table fields &optional srl where-name where-value
+ &key (lrl "KCUILRL") single distinct order like)
+ (concatenate
+ 'string
+ (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
+ (if distinct "distinct " "") fields table)
+ (if where-name (format nil " where ~:@(~A~)" where-name) "")
+ (if where-name
+ (format nil
+ (typecase where-value
+ (number "='~D'")
+ (null " is null")
+ (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" "")))
+
+
+(defmacro umlisp-query (table fields srl where-name where-value
+ &key (lrl "KCUILRL") single distinct order like
+ (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"
- (when (or (not where-name) where-value)
- (mutex-sql-query
- (query-string table fields srl where-name where-value
- :lrlname lrlname :single single :distinct distinct :terminal terminal :like like))))
-
-
-(defun query-string (table fields &optional srl where-name where-value
- &key (lrlname "KCUILRL") single distinct terminal like)
- (let ((qs (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
- (if distinct "distinct " "")
- fields table)))
- (when where-name
- (setq qs (concatenate 'string qs
- (format nil
- (if (stringp where-value)
- (if like
- " where ~A like '%~A%'"
- " where ~A='~A'")
- " where ~A=~A")
- where-name where-value))))
- (when srl
- (setq qs (concatenate 'string qs (format nil " and ~:@(~A~) <= ~D"
- lrlname srl))))
- (when terminal
- (setq qs (concatenate 'string qs " " terminal)))
- (when single
- (setq qs (concatenate 'string qs " limit 1")))
- qs))
+ `(,query-cmd
+ (query-string ,table ,fields ,srl ,where-name ,where-value
+ :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
+
+(defmacro umlisp-query-eval (table fields srl where-name where-value
+ &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-eval ,table ,fields ,srl ,where-name ,where-value
+ :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
+
+;; only WHERE-VALUE and SRL are evaluated
+(defmacro collect-umlisp-query ((table fields srl where-name where-value
+ &key (lrl "KCUILRL") distinct single
+ order like (query-cmd 'mutex-sql-query))
+ &body body)
+ (let ((value (gensym))
+ (r (gensym)))
+ (if single
+ `(let* ((,value ,where-value)
+ (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
+ :lrl ,lrl :single ,single
+ :distinct ,distinct :order ,order
+ :like ,like
+ :query-cmd ,query-cmd))))
+ ,@(unless where-name `((declare (ignore ,value))))
+ (when tuple
+ (destructuring-bind ,fields tuple
+ ,@body)))
+ `(let ((,value ,where-value))
+ ,@(unless where-name `((declare (ignore ,value))))
+ (let ((,r '()))
+ (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
+ :lrl ,lrl :single ,single :distinct ,distinct
+ :order ,order :like ,like))
+ (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)
+ 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)
+ &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))))
+ (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))
+ (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)
+ 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-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 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 (car tuple)
- :lrl (ensure-integer (cadr tuple)))))
-
+ (ensure-cui-integer cui)
+ (unless cui (return-from find-ucon-cui nil))
+
+ (let ((tuple (car (mutex-sql-query
+ (format nil
+ "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A"
+ cui (if srl (format nil " AND SRL<=~D" srl) ""))))))
+ (unless tuple
+ (setq tuple (car (mutex-sql-query
+ (format nil
+ "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D"
+ cui (if srl (format nil " AND SRL<=~D" srl) nil))))))
+ (unless tuple
+ (return-from find-ucon-cui nil))
+ (make-instance 'ucon :cui cui :pfstr (second tuple)
+ :lrl (ensure-integer (first tuple)))))
(defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*))
"Find ucon for a cui"
- (with-umlisp-query ('mrcon '(kcuilrl) srl 'cui (parse-cui cui) :single t)
- (make-instance 'ucon :cui (parse-cui cui)
- :lrl (ensure-integer (car tuple))
+ (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)))
(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)
- (car tuple)))
+ (ensure-cui-integer cui)
+ (or
+ (caar (mutex-sql-query
+ (format nil "SELECT DISTINCT str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A LIMIT 1"
+ cui (if srl (format nil " AND SRL<=~D" srl) ""))))
+ (caar (mutex-sql-query
+ (format nil "SELECT DISTINCT str FROM MRCONSO WHERE CUI=~D~A LIMIT 1"
+ cui (if srl (format nil " AND SRL<=~D" srl) ""))))))
(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)
- (destructuring-bind (cui pfstr lrl) tuple
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer lrl)))))
+ (ensure-lui-integer lui)
+ (collect-umlisp-query (mrconso (cui kcuilrl) srl lui lui
+ :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
+ :lrl (ensure-integer kcuilrl)))
+ (unless lui (return-from find-ucon-lui nil))
+
+ (let ((tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D AND KPFENG=1~A ORDER BY kcuilrl ASC LIMIT 1"
+ lui (if srl (format nil " AND SRL<=~D" srl) "")))))
+ (unless tuple
+ (setq tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D~A ORDER BY kcuilrl ASC LIMIT 1"
+ lui (if srl (format nil " AND SRL<=~D" srl) "")))))
+ (unless tuple
+ (return-from find-ucon-lui nil))
+ (make-instance 'ucon :cui (first tuple) :pfstr (third tuple)
+ :lrl (ensure-integer (third tuple)))))
(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)
- (destructuring-bind (cui pfstr lrl) tuple
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer lrl)))))
+ (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-sui-integer aui)
+ (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
+ :lrl (ensure-integer kcuilrl))))
(defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
"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)))
- (destructuring-bind (cui pfstr lrl) tuple
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer lrl))))))
+ (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)))))
(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)
- (destructuring-bind (cui pfstr lrl) tuple
- (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer lrl)))))
+ (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 :terminal "order by 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 :terminal "order by 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) :lrlname "KSRL")
- (destructuring-bind (sab def) tuple
- (make-instance 'udef :sab sab :def def))))
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
+ (make-instance 'udef :sab sab :def def :suppress suppress)))
+
+(defun find-udoc-key (key)
+ "Return list of abbreviation documentation for a key"
+ (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
+ (make-instance 'udoc :key key :value value :type type :expl expl)))
+
+(defun find-udoc-value (value)
+ "Return abbreviation documentation"
+ (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
+ (make-instance 'udoc :key dockey :value value :type type :expl expl)))
+
+(defun find-udoc-key-value (key value)
+ (let ((tuple (car (mutex-sql-query
+ (format nil "SELECT TYPE,EXPL FROM MRDOC WHERE DOCKEY='~A' AND VALUE='~A'"
+ key value)))))
+ (when tuple
+ (make-instance 'udoc :key key :value value :type (first tuple) :expl (second tuple)))))
+
+(defun find-udoc-all ()
+ "Return all abbreviation documentation"
+ (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
+ (make-instance 'udoc :key dockey :value value :type type :expl expl)))
(defun find-usty-cui (cui &key (srl *current-srl*))
"Return a list of usty for cui"
- (with-umlisp-query ('mrsty '(tui sty) srl 'cui (parse-cui cui) :lrlname "KLRL")
- (destructuring-bind (tui sty) tuple
- (make-instance 'usty :tui (ensure-integer tui) :sty sty))))
+ (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 :lrlname 'klrl :like t :distinct t)
- (destructuring-bind (tui sty) tuple
- (make-instance 'usty :tui (ensure-integer tui) :sty sty))))
+ (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*))
"Return a list of urel for cui"
- (with-umlisp-query ('mrrel '(rel cui2 rela sab sl mg kpfstr2) srl 'cui1 (parse-cui cui) :lrlname "KSRL")
- (destructuring-bind (rel cui2 rela sab sl mg pfstr2) tuple
- (make-instance 'urel :cui1 (parse-cui cui) :rel rel :cui2 (ensure-integer cui2) :rela rela
- :sab sab :sl sl :mg mg :pfstr2 pfstr2))))
+ (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 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))
(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) :lrlname "KSRL")
- (destructuring-bind (rel cui1 rela sab sl mg pfstr2) tuple
- (make-instance 'urel :cui2 (parse-cui cui2) :rel rel :cui1 (ensure-integer cui1) :rela rela
- :sab sab :sl sl :mg mg :pfstr2 pfstr2))))
+ (ensure-cui-integer cui2)
+ (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
+ srl cui2 cui2 :lrl "KSRL")
+ (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2) :stype2 stype2 :rui rui :srui srui
+ :stype1 stype1 :cui1 (ensure-integer cui1) :aui1 (ensure-integer aui1)
+ :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*))
"Return a list of ucoc for cui"
- (with-umlisp-query ('mrcoc '(cui2 soc cot cof coa kpfstr2) srl 'cui1 (parse-cui cui)
- :lrlname "KSRL" :terminal "order by COF asc")
- (destructuring-bind (cui2 soc cot cof coa pfstr2) tuple
- (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 pfstr2))))
+ (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 (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*))
"Return a list of ucoc for cui2"
- (with-umlisp-query ('mrcoc '(cui1 soc cot cof coa kpfstr2) srl 'cui2 (parse-cui cui2)
- :lrlname "KSRL" :terminal "order by COF asc")
- (destructuring-bind (cui1 soc cot cof coa pfstr2) tuple
- (setq cui2 (ensure-integer cui2))
- (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 pfstr2))))
+ (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 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*))
"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) :lrlname "KLRL")
- (destructuring-bind (isn fr un sui sna soui) tuple
- (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) :lrlname 'ksrl)
- (destructuring-bind (sab rel atx) tuple
- (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) :lrlname 'kluilrl
- :distinct t)
- (destructuring-bind (lui lat ts lrl) tuple
- (make-instance 'uterm :lui (ensure-integer lui) :cui (parse-cui cui)
- :lat lat :ts ts :lrl (ensure-integer lrl)))))
+ (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)
- :lrlname 'kluilrl :distinct t)
- (destructuring-bind (cui lat ts lrl) tuple
- (make-instance 'uterm :cui (ensure-integer cui) :lui (parse-lui lui)
- :lat lat :ts ts :lrl (ensure-integer lrl)))))
-
+ (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))
- :lrlname 'kluilrl :single t)
- (destructuring-bind (lat ts lrl) tuple
- (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts :lrl (ensure-integer lrl)))))
+ (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) :lrlname 'lrl)
- (destructuring-bind (sui stt str lrl) tuple
- (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)
+ (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 (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) :lrlname 'lrl :single t)
- (destructuring-bind (lui stt str lrl) tuple
- (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)
+ (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))))
(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) :lrlname 'lrl)
- (destructuring-bind (cui lui stt str lrl) tuple
- (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)))))
-
+ (ensure-sui-integer sui)
+ (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
+ :lrl ksuilrl)
+ (make-instance 'ustr :sui sui :cui cui :stt stt :str str
+ :cuisui (make-cuisui (ensure-integer cui) sui)
+ :suppress suppress
+ :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
+
(defun find-ustr-sab (sab &key (srl *current-srl*))
"Return the list of ustr for sab"
- (with-umlisp-query ('mrso '(kcuisui) srl 'sab sab :lrlname 'srl)
- (let ((cuisui (ensure-integer (car tuple))))
- (apply #'find-ustr-cuisui
+ (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))))))
+ (multiple-value-list (decompose-cuisui cuisui))
+ (list :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 :lrlname 'lrl :distinct t
- :terminal "order by 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 :lrlname 'lrl :single t)
- (car tuple)))
+ (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) :lrlname 'srl)
- (destructuring-bind (sab code srl tty) tuple
- (make-instance 'uso :sab sab :code code :srl srl :tty tty))))
+ (ensure-sui-integer sui)
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui
+ (make-cuisui cui sui) :lrl srl)
+ (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
+ :cui cui :sui sui :saui saui :sdui sdui :scui scui)))
+
+(defun find-uso-aui (aui &key (srl *current-srl*))
+ (ensure-sui-integer aui)
+ (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui) srl aui
+ aui :lrl srl :single t)
+ (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
+ :sui sui :saui saui :sdui sdui :scui scui)))
(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
- (with-umlisp-query ('mrcxt '(sab code cxn cxl rnk cxs cui2 hcd rela cx) srl 'kcuisui
- (make-cuisui cui sui) :lrlname 'ksrl)
- (destructuring-bind (sab code cxn cxl rnk cxs cui2 hcd rela xc) tuple
- (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)))))
+ (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))))
+
+(defun find-uhier-cui (cui &key (srl *current-srl*))
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
+ srl cui cui :lrl ksrl)
+ (make-instance 'uhier :cui cui :aui (ensure-integer aui)
+ :cxn (ensure-integer cxn)
+ :paui (ensure-integer paui)
+ :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
+
+(defun find-uhier-all (&key (srl *current-srl*))
+ (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
+ srl nil nil :lrl ksrl)
+ (make-instance 'uhier :cui cui :aui (ensure-integer aui)
+ :cxn (ensure-integer cxn)
+ :paui (ensure-integer paui)
+ :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
(defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
- (let ((ls (format nil "select CODE,ATN,SAB,ATV from MRSAT where ")))
+ (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)))
- (let ((usats '()))
- (dolist (tuple (mutex-sql-query ls))
- (destructuring-bind (code atn sab atv) tuple
- (push (make-instance 'usat :code code :atn atn :sab sab :atv atv)
- usats)))
- (nreverse usats))))
-
+ (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 (car tuple))))
+ (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)
- (make-instance 'usty :tui (ensure-integer (car tuple)) :sty sty)))
+ (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)
- (find-usty-tui (car tuple))))
+ (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
+ (find-usty-tui tui)))
(defun find-usab-all ()
"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)
- (destructuring-bind
- (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) tuple
- (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))))
+ (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)
"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)
- (destructuring-bind
- (vcui rcui vsab rsab son sf sver mstart mend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) tuple
- (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))))
+ (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)
+ (make-instance 'usab :vcui (ensure-integer vcui)
+ :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
+ :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
+ :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
+ :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
+ :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
+ :curver curver :sabin sabin
+ :ssn ssn :scit scit)))
(defun find-usab-rsab (rsab)
"Find usab for rsab"
- (find-usab-by-key "RSAB" rsab))
+ (find-usab-by-key 'rsab rsab))
(defun find-usab-vsab (vsab)
"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)))
+
;;;; 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) :lrlname 'klrl :terminal "order by cui desc")
- (find-ucon-cui (ensure-integer (car tuple)) :srl srl)))
-
+ (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"
- (let ((ucons '())
- (ls (format nil "select distinct cui from MRXW_ENG where wd~A'~A'"
- (if like " LIKE " "=")
- word)))
- (when srl (string-append ls (format nil " and KLRL <= ~d" srl)))
- (string-append ls " order by cui desc")
- (dolist (tuple (mutex-sql-query ls))
- (push (find-ucon-cui (car tuple) :srl srl) ucons))
- ucons))
+ (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"
- (let ((ucons '())
- (ls (format nil "select distinct cui from MRXNW_ENG where nwd~A'~A'"
- (if like " LIKE " "=")
- word)))
- (when srl (string-append ls (format nil " and KLRL <= ~d" srl)))
- (string-append ls " order by cui desc")
- (dolist (tuple (mutex-sql-query ls))
- (push (find-ucon-cui (car tuple) :srl srl) ucons))
- ucons))
+ (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-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 (srl *current-srl*))
"Return list of ustrs that match word"
- (with-umlisp-query ('mrxw_eng '(cui sui) srl 'wd word
- :lrlname 'klrl
- :terminal "order by cui desc, sui desc")
- (destructuring-bind (cui sui) tuple
- (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl))))
+ (collect-umlisp-query (mrxw_eng (cui sui) srl wd word :lrl klrl
+ :order (cui asc sui asc))
+ (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
(defun find-ustr-normalized-word (word &key (srl *current-srl*))
"Return list of ustrs that match word"
- (with-umlisp-query ('mrxnw_eng '(cui sui) srl 'nwd word :lrlname 'klrl
- :terminal "order by cui desc, sui desc")
- (destructuring-bind (cui sui) tuple
- (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) ;srl srl))))
+ (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)))
+
+(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 (cui sui) srl wd word :lrl klrl
+ :order (cui asc sui asc))
+ (find-ustr-cuisui (ensure-integer cui) (ensure-integer sui) :srl srl)))
;; Special tables
(defun find-usrl-all ()
- (with-umlisp-query ('usrl '(sab srl) nil nil nil :terminal "order by sab desc")
- (destructuring-bind (sab srl) tuple
- (make-instance 'usrl :sab sab :srl (ensure-integer srl)) usrls)))
+ (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)
+ (let ((uobjs '()))
+ (dolist (word (delimited-string-to-list str #\space))
+ (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl))))
+ (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)
+ (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
+ #'cui srl only-exact-if-match limit))
+
+(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)
+ (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
+ #'sui srl only-exact-if-match limit))
+
+(defun sort-score-pfstr-str (str uobjs)
"Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
- (sort-score-umlsclass-str 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"
"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)
- (make-instance 'lexterm :eui eui :wrd (car tuple))))
+ (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)
- (make-instance 'lexterm :eui (ensure-integer (car tuple))
+ (collect-umlisp-query (lrwd (eui) nil wrd wrd)
+ (make-instance 'lexterm :eui (ensure-integer eui)
:wrd (copy-seq wrd))))
;; LEX SQL Read functions
(defun find-labr-eui (eui)
- (with-umlisp-query ('lrabr '(bas abr eui2 bas2) nil 'eui eui)
- (destructuring-bind (bas abr eui2 bas2) tuple
- (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
- :eui2 (ensure-integer eui2)))))
+ (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))))
(defun find-labr-bas (bas)
- (with-umlisp-query ('labr '(eui abr eui2 bas2) nil 'bas bas)
- (destructuring-bind (eui abr eui2 bas2) tuple
- (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
- :bas (copy-seq bas) :eui2 (ensure-integer eui2)))))
+ (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))))
(defun find-lagr-eui (eui)
- (with-umlisp-query ('lragr '(str sca agr cit bas) nil 'eui eui)
- (destructuring-bind (str sca agr cit bas) tuple
- (make-instance 'lagr :eui eui :str str :sca sca :agr agr
- :cit cit :bas bas))))
+ (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)))
(defun find-lcmp-eui (eui)
- (with-umlisp-query ('lrcmp '(bas sca com) nil 'eui eui)
- (destructuring-bind (bas sca com) tuple
- (make-instance 'lcmp :eui eui :bas bas :sca sca :com com))))
+ (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)
- (destructuring-bind (bas sca psnmod fea) tuple
- (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psnmod :fea fea))))
+ (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)
- (destructuring-bind (bas sca eui2 bas2 sca2) tuple
- (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
- :eui2 (ensure-integer eui2)))))
+ (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))))
(defun find-lprn-eui (eui)
- (with-umlisp-query ('lrprn '(bas num gnd cas pos qnt fea) nil 'eui eui)
- (destructuring-bind (bas num gnd cas pos qnt fea) tuple
- (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
- :cas cas :pos pos :qnt qnt :fea fea))))
+ (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)))
(defun find-lprp-eui (eui)
- (with-umlisp-query ('lrprp '(bas str sca fea) nil 'eui eui)
- (destructuring-bind (bas str sca fea) tuple
- (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea))))
+ (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)
- (destructuring-bind (spv bas) tuple
- (make-instance 'lspl :eui eui :spv spv :bas bas))))
+ (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)
- (destructuring-bind (bas sca typ) tuple
- (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ))))
+ (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 (car tuple)))))
+ (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)
- (destructuring-bind (rt styrl stnrtn def ex un rh abr rin) tuple
- (make-instance 'sdef :rt rt :ui ui :styrl styrl :stnrtn stnrtn
- :def def :ex ex :un un :rh rh :abr abr :rin rin))))
+ (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)))
(defun find-sstre1-ui (ui)
- (with-umlisp-query ('srstre1 '(ui2 ui3) nil 'ui ui)
- (destructuring-bind (ui2 ui3) tuple
- (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
- :ui3 (ensure-integer ui3)))))
+ (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
+ (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
+ :ui3 (ensure-integer ui3))))
(defun find-sstre1-ui2 (ui2)
- (with-umlisp-query ('srstre1 '(ui ui3) nil 'ui2 ui2)
- (destructuring-bind (ui ui3) tuple
- (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
- :ui3 (ensure-integer ui3)))))
+ (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
+ (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
+ :ui3 (ensure-integer ui3))))
(defun find-sstr-rl (rl)
- (with-umlisp-query ('srstre '(sty_rl sty_rl2 ls) nil 'rl rl)
- (destructuring-bind (styrl styrl2 ls) tuple
- (make-instance 'sstr :rl rl :styrl styrl :styrl2 styrl2 :ls ls))))
+ (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)
- (destructuring-bind (rl sty2) tuple
- (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2))))
+ (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)
- (destructuring-bind (rl styrl2 ls) tuple
- (make-instance 'sstr :styrl styrl :rl rl :styrl2 styrl2 :ls ls))))
+ (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 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)
+ (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-bsab-sab (sab)
+ (collect-umlisp-query (bonus_sab (name count) nil sab sab :single t)
+ (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
+
+(defun find-bsab-all ()
+ (collect-umlisp-query (bonus_sab (sab name count) nil nil nil :order (sab asc))
+ (make-instance 'bsab :sab sab :name name :hits (ensure-integer count))))
+
+(defun find-btty-tty (tty)
+ (collect-umlisp-query (bonus_tty (name count) nil tty tty :single t)
+ (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
+
+(defun find-btty-all ()
+ (collect-umlisp-query (bonus_tty (tty name count) nil nil nil :order (tty asc))
+ (make-instance 'btty :tty tty :name name :hits (ensure-integer count))))
+
+(defun find-brel-rel (rel)
+ (collect-umlisp-query (bonus_rel (sab sl rel rela count) nil rel rel)
+ (make-instance 'brel :sab sab :sl sl :rel rel :rela rela
+ :hits (ensure-integer count))))
projects / umlisp.git / blobdiff