;;;; *************************************************************************
;;;; FILE IDENTIFICATION
;;;;
-;;;; Name: sql-classes.lisp
-;;;; Purpose: Routines for reading UMLS objects from SQL database
-;;;; Author: 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 1.92 2003/08/27 23:55:17 kevin Exp $
+;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D.
,%%fields
,@(when %%where (list %%where))
,@(when %%where
- `((typecase ,where-value
- (fixnum
- (prefixed-fixnum-string ,where-value #\= 10))
- (number
- (concatenate 'string "=" (write-to-string ,where-value)))
- (null
- " is null")
- (t
- (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
+ `((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")))))
(if where-name
(format nil
(typecase where-value
- (number "=~D")
+ (number "='~D'")
(null " is null")
(t
(if like " like '%~A%""='~A'")))
:pfstr kpfstr
:lrl (ensure-integer kcuilrl))))
+(defun find-cui-ucon-all (&key (srl *current-srl*))
+ "Return list of CUIs for all ucons"
+ (collect-umlisp-query (mrcon (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)
:cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl
:mg mg :pfstr2 kpfstr2)))
+(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"
(ensure-cui-integer cui2)
(collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1
cui :lrl klrl :order (cof asc))
(setq cui2 (ensure-integer cui2))
- (when (zerop cui2) (setq cui2 nil))
+ (when (eql 0 cui2) (setq cui2 nil))
(make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2)
:soc soc :cot cot :cof (ensure-integer cof) :coa coa
:pfstr2 kpfstr2)))
(ensure-sui-integer sui)
(let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
(cond
- (sui (string-append ls "KCUISUI="
- (integer-string (make-cuisui cui sui) 14)))
- (lui (string-append ls "KCUILUI="
+ (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")))
+ "' 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 " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
(loop for tuple in (mutex-sql-query ls) collect
(defun find-usab-all ()
"Find usab for a key"
- (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta
+ (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) 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
+ :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
(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 mstart
- mend imeta rmeta slc scc srl tfr cfr cxty
+ (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 :mstart mstart :mend mend :imeta imeta
+ :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
(defun make-ustats ()
(with-sql-connection (conn)
- (sql-execute "drop table if exists USTATS" 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)
conn))
(defun find-ustats-all (&key (srl *current-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))))
-
+ (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))))
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