;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2003 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.
(setq *current-srl* srl))
(defmacro query-string (table fields &optional srl where-name where-value
- &key (lrl "KCUILRL") single distinct order like)
- (let* ((%%fields (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
- (if distinct "distinct " "") fields table))
- (%%order (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}"
+ &key (lrl "KCUILRL") single distinct order like limit
+ filter)
+ (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
+ (if distinct "DISTINCT " "") fields table))
+ (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}"
order)
""))
- (%%lrl (format nil " and ~:@(~A~)<=" lrl))
+ (%%lrl (format nil " AND ~:@(~A~)<=" lrl))
(%%where (when where-name
- (format nil " where ~:@(~A~)~A" where-name
- (if like " like " "")))))
- `(concatenate
- 'string
- ,%%fields
- ,@(when %%where (list %%where))
- ,@(when %%where
- `((typecase ,where-value
- #+ignore
- (fixnum
- (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
- (number
- (concatenate 'string "='" (write-to-string ,where-value) "'"))
- (null
- " is null")
- (t
- (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
- (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
- ,@(when %%order (list %%order))
- ,@(when single (list " limit 1")))))
+ (format nil " WHERE ~:@(~A~)~A" where-name
+ (if like " like " ""))))
+ (%filter (gensym "FILTER-"))
+ (%single (gensym "SINGLE-"))
+ (%limit (gensym "LIMIT-")))
+ `(let ((,%limit ,limit)
+ (,%single ,single)
+ (,%filter ,filter))
+ (concatenate
+ 'string
+ ,%%fields
+ ,@(when %%where (list %%where))
+ ,@(when %%where
+ `((typecase ,where-value
+ #+ignore
+ (fixnum
+ (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
+ (number
+ (concatenate 'string "='" (write-to-string ,where-value) "'"))
+ (null
+ " IS NULL")
+ (t
+ (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
+ (if ,%filter (concatenate 'string
+ ,(if %%where " AND " " WHERE ")
+ ,%filter) "")
+ (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
+ ,@(when %%order (list %%order))
+ (cond
+ ((and ,%single ,%limit)
+ (error "Can't set single and limit"))
+ (,%single
+ " LIMIT 1")
+ (,%limit
+ (format nil " LIMIT ~D" ,%limit))
+ (t
+ ""))))))
(defun query-string-eval (table fields &optional srl where-name where-value
- &key (lrl "KCUILRL") single distinct order like)
+ &key (lrl "KCUILRL") single distinct order like limit filter)
+ (when single (setq limit 1))
(concatenate
'string
- (format nil "select ~A~{~:@(~A~)~^,~} from ~:@(~A~)"
- (if distinct "distinct " "") fields table)
- (if where-name (format nil " where ~:@(~A~)" where-name) "")
+ (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
+ (if distinct "DISTINCT " "") fields table)
+ (if where-name (format nil " WHERE ~:@(~A~)" where-name) "")
(if where-name
(format nil
(typecase where-value
(number "='~D'")
- (null " is null")
+ (null " IS NULL")
(t
- (if like " like '%~A%""='~A'")))
+ (if like " LINK '%~A%""='~A'")))
where-value)
"")
- (if srl (format nil " and ~:@(~A~)<=~D" lrl srl) "")
- (if order (format nil " order by ~{~:@(~A~) ~(~A~)~^,~}" order) "")
- (if single " limit 1" "")))
+ (if filter (concatenate 'string " AND " filter) nil)
+ (if srl (format nil " AND ~:@(~A~)<=~D" lrl srl) "")
+ (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}" order) "")
+ (if limit (format nil " LIMIT ~D" limit) "")))
(defmacro umlisp-query (table fields srl where-name where-value
&key (lrl "KCUILRL") single distinct order like
- (query-cmd 'mutex-sql-query))
+ limit filter (query-cmd 'mutex-sql-query))
"Query the UMLisp database. Return a list of umlisp objects whose name
is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
`(,query-cmd
- (query-string ,table ,fields ,srl ,where-name ,where-value
- :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like)))
+ (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)
+ &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)))
+ (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))
+ order like (query-cmd 'mutex-sql-query)
+ filter limit)
&body body)
(let ((value (gensym))
- (r (gensym)))
+ (r (gensym)))
(if single
- `(let* ((,value ,where-value)
- (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
- :lrl ,lrl :single ,single
- :distinct ,distinct :order ,order
- :like ,like
- :query-cmd ,query-cmd))))
- ,@(unless where-name `((declare (ignore ,value))))
- (when tuple
- (destructuring-bind ,fields tuple
- ,@body)))
+ (if (and limit (> limit 1))
+ (error "Can't set limit along with single.")
+ `(let* ((,value ,where-value)
+ (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
+ :lrl ,lrl :single ,single
+ :distinct ,distinct :order ,order
+ :like ,like :filter ,filter
+ :query-cmd ,query-cmd))))
+ ,@(unless where-name `((declare (ignore ,value))))
+ (when tuple
+ (destructuring-bind ,fields tuple
+ ,@body))))
`(let ((,value ,where-value))
,@(unless where-name `((declare (ignore ,value))))
(let ((,r '()))
(dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single :distinct ,distinct
- :order ,order :like ,like))
+ :order ,order :filter ,filter :like ,like
+ :limit ,limit))
(push (destructuring-bind ,fields tuple ,@body) ,r))
(nreverse ,r))
#+ignore
(loop for tuple in
(umlisp-query ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single :distinct ,distinct
- :order ,order :like ,like)
+ :order ,order :like ,like :filter ,filter :limit ,limit)
collect (destructuring-bind ,fields tuple ,@body))))))
(defmacro collect-umlisp-query-eval ((table fields srl where-name where-value
&key (lrl "KCUILRL") distinct single
- order like)
+ order like filter limit)
&body body)
(let ((value (gensym))
(r (gensym))
(tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single
:distinct ,distinct :order ,order
- :like ,like))))
+ :like ,like :filter ,filter
+ :limit ,limit))))
(when tuple
(destructuring-bind ,eval-fields tuple
,@body)))
(,r '()))
(dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single :distinct ,distinct
- :order ,order :like ,like))
+ :order ,order :like ,like
+ :filter ,filter :limit ,limit))
(push (destructuring-bind ,eval-fields tuple ,@body) ,r))
(nreverse ,r)
#+ignore
(loop for tuple in
(umlisp-query-eval ,table ,fields ,srl ,where-name ,value
:lrl ,lrl :single ,single :distinct ,distinct
- :order ,order :like ,like)
+ :order ,order :like ,like :filter ,filter
+ :limit ,limit)
collect (destructuring-bind ,eval-fields tuple ,@body))))))
;;;
(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))
(setq ,eui (parse-eui ,eui))
,eui))
-(defun find-ucon-cui (cui &key (srl *current-srl*))
- "Find ucon for a cui"
+(defun make-ucon-cui (cui)
(ensure-cui-integer cui)
- (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl cui cui :single t)
- (make-instance 'ucon :cui cui :pfstr kpfstr
- :lrl (ensure-integer kcuilrl))))
-
-(defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*))
+ (when cui
+ (make-instance 'ucon :cui cui)))
+
+(defun find-ucon-cui (cui &key (srl *current-srl*) without-pfstr)
"Find ucon for a cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
- (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
- :pfstr nil)))
+ (unless cui (return-from find-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-pfstr-cui (cui &key (srl *current-srl*))
"Find preferred string for a cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t)
- kpfstr))
-
+ (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"
(ensure-lui-integer lui)
- (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui
- :distinct t)
- (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
- :lrl (ensure-integer kcuilrl))))
+ (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"
(ensure-sui-integer sui)
- (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t)
- (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ (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 kpfstr kcuilrl) srl aui aui :distinct t)
- (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ (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 (cui sui &key (srl *current-srl*))
(ensure-cui-integer cui)
(ensure-sui-integer sui)
(when (and cui sui)
- (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl kcuisui
+ (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui
(make-cuisui cui sui))
(make-instance 'ucon :cui cui
- :pfstr kpfstr
+ :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"
- (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t)
- (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ (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 (tuple)
- (destructuring-bind (cui pfstr cuilrl) tuple
+ (destructuring-bind (cui cuilrl) tuple
(make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
- :lrl (ensure-integer cuilrl))))
- (query-string mrconso (cui kpfstr kcuilrl) srl nil nil
+ :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 kpfstr kcuilrl) srl nil nil :order (cui asc)
+ (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
:distinct t)
(make-instance 'ucon :cui (ensure-integer cui)
- :pfstr kpfstr
+ :pfstr (find-pfstr-cui cui)
:lrl (ensure-integer kcuilrl))))
(defun find-cui-ucon-all (&key (srl *current-srl*))
(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 (tuple)
- (destructuring-bind (cui pfstr cuilrl) tuple
+ (destructuring-bind (cui cuilrl) tuple
(funcall fn (make-instance 'ucon :cui (ensure-integer cui)
- :pfstr pfstr
+ :pfstr (find-pfstr-cui cui)
:lrl (ensure-integer cuilrl)))))
- (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
:distinct t)
:database db)))
(defun find-udoc-key (key)
"Return list of abbreviation documentation for a key"
(collect-umlisp-query (mrdoc (value type expl) nil dockey key)
- (make-instance 'udoc :key key :value value :type type :expl expl)))
+ (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
(defun find-udoc-value (value)
"Return abbreviation documentation"
(collect-umlisp-query (mrdoc (dockey type expl) nil value value)
- (make-instance 'udoc :key dockey :value value :type type :expl expl)))
-
-(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)))))
-
+ (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 :key dockey :value value :type type :expl expl)))
+ (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
(defun find-usty-cui (cui &key (srl *current-srl*))
"Return a list of usty for cui"
: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 kpfstr2)
- srl cui1 cui :lrl "KSRL")
- (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
+ (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 rui :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
- :suppress suppress :cvf cvf :pfstr2 kpfstr2)))
+ :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"
(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
"Return a list of urel for cui2"
(ensure-cui-integer cui2)
- (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf kpfstr2)
+ (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
srl cui2 cui2 :lrl "KSRL")
- (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2) :stype2 stype2 :rui rui :srui srui
- :stype1 stype1 :cui1 (ensure-integer cui1) :aui1 (ensure-integer aui1)
+ (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
+ :stype2 stype2 :rui (ensure-integer rui) :srui srui
+ :stype1 stype1 :cui1 (ensure-integer cui1)
+ :aui1 (ensure-integer aui1)
:rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
- :pfstr2 kpfstr2)))
+ :pfstr2 (find-pfstr-cui cui2))))
(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
(ensure-cui-integer cui2)
(defun find-ucoc-cui (cui &key (srl *current-srl*))
"Return a list of ucoc for cui"
(ensure-cui-integer cui)
- (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa kpfstr2) srl cui1
+ (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 kpfstr2)))
+ :pfstr2 (find-pfstr-cui cui2))))
(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
"Return a list of ucoc for cui2"
(ensure-cui-integer cui2)
- (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa kpfstr2) srl 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 kpfstr2)))
+ :pfstr2 (find-pfstr-cui cui2))))
(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
"List of ucon with co-occurance cui2"
(ensure-cui-integer cui2)
- (mapcar
+ (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"
- (ensure-cui-integer cui)
- (collect-umlisp-query (mrlo (isn fr un sui sna soui) srl cui cui
- :lrl "KLRL")
- (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un
- :sui (ensure-integer sui) :sna sna :soui soui)))
-
(defun find-uterm-cui (cui &key (srl *current-srl*))
"Return a list of uterm for cui"
(defun find-uterm-lui (lui &key (srl *current-srl*))
"Return a list of uterm for lui"
(ensure-lui-integer lui)
- (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
+ (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))))
:cuisui (make-cuisui (ensure-integer cui) sui)
:suppress suppress
:lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
-
+
(defun find-ustr-sab (sab &key (srl *current-srl*))
"Return the list of ustr for sab"
(collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
(let ((cuisui (ensure-integer kcuisui)))
- (apply #'find-ustr-cuisui
+ (apply #'find-ustr-cuisui
(append
(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 (tuple)
- (destructuring-bind (cui lui sui stt ksuilrl suppress pfstr) 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 pfstr
+ :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 kpfstr) srl nil nil :lrl ksuilrl
+ (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
:distinct t
:order (sui asc))
:database db)))
(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
(ensure-sui-integer sui)
(ensure-cui-integer cui)
- (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui
- (make-cuisui cui sui) :lrl srl)
+ (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str)
+ srl kcuisui (make-cuisui cui sui) :lrl srl)
(make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
- :cui cui :sui sui :saui saui :sdui sdui :scui scui)))
+ :cui cui :sui sui :saui saui :sdui sdui :scui scui
+ :lat lat :str str)))
+
+(defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui)
+ srl cui cui :lrl srl :limit limit
+ :filter (when english-only "LAT='ENG'"))
+ (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
+ :cui cui :sui sui :saui saui :sdui sdui :scui scui
+ :lat lat :str str)))
(defun find-uso-aui (aui &key (srl *current-srl*))
(ensure-sui-integer aui)
- (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui) srl aui
- aui :lrl srl :single t)
+ (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat
+ str) srl aui aui :lrl srl :single t)
(make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
- :sui sui :saui saui :sdui sdui :scui scui)))
+ :sui sui :saui saui :sdui sdui :scui scui :lat lat
+ :str str)))
(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
(ensure-cui-integer cui)
(ensure-sui-integer sui)
- (collect-umlisp-query (mrcxt (sab code cxn cxl cxs cui2 hcd rela xc)
+ (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
+ (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))))
(ensure-cui-integer cui)
(ensure-lui-integer lui)
(ensure-sui-integer sui)
- (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
+ (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE "))
(cond
(sui (string-append ls "KCUISUI='"
(integer-string (make-cuisui cui sui) 14)
"' and lui='0' and sui='0'")))
(when srl
(string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
- (loop for tuple in (mutex-sql-query ls) collect
+ (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)))))
(find-usty-tui tui)))
(defun find-usab-all ()
- "Find usab for a key"
+ "Return all usab objects"
(collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
rmeta slc scc srl tfr cfr cxty ttyl atnl lat
cenc curver sabin ssn scit) nil nil nil)
- (make-instance 'usab :vcui (ensure-integer vcui)
+ (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)
(defun find-usab-by-key (key-name key)
"Find usab for a key"
(collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
- vend imeta rmeta slc scc srl tfr cfr cxty
- ttyl atnl lat cenc curver sabin)
- 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)))
+ 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"
: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*))
(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"
(collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
;;; Multiword lookup and score functions
(defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
- only-exact-if-match)
+ 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
+ (let ((sorted
(funcall sort-fun str
(delete-duplicates uobjs :test #'= :key key))))
- (if (and (plusp (length sorted))
- only-exact-if-match
- (multiword-match str (pfstr (first sorted))))
- (first sorted)
- sorted))))
-
+ (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))
+ (only-exact-if-match t)
+ limit)
(find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
- #'cui srl only-exact-if-match))
+ #'cui srl only-exact-if-match limit))
(defun find-uterm-multiword (str &key (srl *current-srl*)
- (only-exact-if-match t))
+ (only-exact-if-match t)
+ limit)
(find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
- #'lui srl only-exact-if-match))
+ #'lui srl only-exact-if-match limit))
(defun find-ustr-multiword (str &key (srl *current-srl*)
- (only-exact-if-match t))
+ (only-exact-if-match t)
+ limit)
(find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
- #'sui srl only-exact-if-match))
-
+ #'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 uobjs str #'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 find-labr-eui (eui)
(ensure-eui-integer eui)
- (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui 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-ltrm-eui (eui)
(ensure-eui-integer eui)
- (collect-umlisp-query (lrtrm (bas gen) nil eui 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-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 4)
+
+ (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 "Context Count" "MRCXT" "*" "KSRL" 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)
- #+ignore
- (insert-ustats-count conn "Locator Count" "MRLO" "*" "KLRL" 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)
(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"
+ (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"
+ (caar (sql-query (format nil "select count(~a) from ~a"
count-variable table )
conn))))
(t
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))
+ (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*))
(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))))
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