--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: sql-classes.lisp
+;;;; Purpose: Routines for reading UMLS objects from SQL database
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
+;;;;
+;;;; $Id$
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2003 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-orf)
+
+
+(defvar *current-srl* nil)
+(defun current-srl ()
+ *current-srl*)
+(defun current-srl! (srl)
+ (setq *current-srl* srl))
+
+(defmacro query-string (table fields &optional srl where-name where-value
+ &key (lrl "KCUILRL") single distinct order like)
+ (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
+ (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"
+ `(,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"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrcon (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*))
+ "Find ucon for a cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrcon (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"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrcon (kpfstr) srl cui cui :single t)
+ kpfstr))
+
+(defun find-ucon-lui (lui &key (srl *current-srl*))
+ "Find list of ucon for lui"
+ (ensure-lui-integer lui)
+ (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui lui
+ :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ :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 (mrcon (cui kpfstr kcuilrl) srl sui sui :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ :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)
+ (collect-umlisp-query (mrcon (kpfstr kcuilrl) srl kcuisui
+ (make-cuisui cui sui))
+ (make-instance 'ucon :cui cui
+ :pfstr kpfstr
+ :lrl (ensure-integer kcuilrl)))))
+
+(defun find-ucon-str (str &key (srl *current-srl*))
+ "Find ucon that are exact match for str"
+ (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl str str :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr
+ :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
+ 'list
+ #'(lambda (cui pfstr cuilrl)
+ (make-instance 'ucon :cui (ensure-integer cui)
+ :pfstr pfstr
+ :lrl (ensure-integer cuilrl)))
+ (query-string mrcon (cui kpfstr kcuilrl) srl nil nil
+ :order (cui asc) :distinct t)
+ :database db)))
+
+(defun find-ucon-all2 (&key (srl *current-srl*))
+ "Return list of all ucon's"
+ (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ :distinct t)
+ (make-instance 'ucon :cui (ensure-integer cui)
+ :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)
+ (clsql:map-query
+ nil
+ #'(lambda (cui pfstr cuilrl)
+ (funcall fn
+ (make-instance 'ucon :cui (ensure-integer cui)
+ :pfstr pfstr
+ :lrl (ensure-integer cuilrl))))
+ (query-string mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc)
+ :distinct t)
+ :database db)))
+
+
+(defun find-udef-cui (cui &key (srl *current-srl*))
+ "Return a list of udefs for cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrdef (sab def) srl cui cui :lrl "KSRL")
+ (make-instance 'udef :sab sab :def def)))
+
+(defun find-usty-cui (cui &key (srl *current-srl*))
+ "Return a list of usty for cui"
+ (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"
+ (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"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1
+ cui :lrl "KSRL")
+ (make-instance 'urel :cui1 cui :rel rel
+ :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 (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2
+ cui2 :lrl "KSRL")
+ (make-instance 'urel :cui2 cui2 :rel rel
+ :cui1 (ensure-integer cui1) :rela rela :sab sab :sl sl
+ :mg mg :pfstr2 kpfstr2)))
+
+(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
+ (ensure-cui-integer cui2)
+ (loop for cui in (remove-duplicates
+ (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
+ collect (find-ucon-cui cui :srl srl)))
+
+(defun find-ucoc-cui (cui &key (srl *current-srl*))
+ "Return a list of ucoc for cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) 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 :cui2 (ensure-integer cui2)
+ :soc soc :cot cot :cof (ensure-integer cof) :coa coa
+ :pfstr2 kpfstr2)))
+
+(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 soc cot cof coa kpfstr2) srl cui2
+ cui2 :lrl klrl :order (cof asc))
+ (when (zerop cui2) (setq cui2 nil))
+ (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
+ :soc soc :cot cot :cof (ensure-integer cof) :coa coa
+ :pfstr2 kpfstr2)))
+
+(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
+ "List of ucon with co-occurance cui2"
+ (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"
+ (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-uatx-cui (cui &key (srl *current-srl*))
+ "Return a list of uatx for cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mratx (sab rel atx) srl cui cui :lrl ksrl)
+ (make-instance 'uatx :sab sab :rel rel :atx atx)))
+
+
+(defun find-uterm-cui (cui &key (srl *current-srl*))
+ "Return a list of uterm for cui"
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrcon (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"
+ (ensure-lui-integer lui)
+ (collect-umlisp-query (mrcon (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"
+ (ensure-cui-integer cui)
+ (ensure-lui-integer lui)
+ (collect-umlisp-query (mrcon (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"
+ (ensure-cui-integer cui)
+ (ensure-lui-integer lui)
+ (collect-umlisp-query (mrcon (sui stt str lrl) srl kcuilui
+ (make-cuilui cui lui) :lrl lrl)
+ (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
+ :cuisui (make-cuisui cui sui) :stt stt :str str
+ :lrl (ensure-integer lrl))))
+
+(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
+ "Return the single ustr for cuisui"
+ (ensure-cui-integer cui)
+ (ensure-sui-integer sui)
+ (collect-umlisp-query (mrcon (lui stt str lrl) srl kcuisui
+ (make-cuisui cui sui) :lrl lrl :single t)
+ (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui)
+ :lui (ensure-integer lui) :stt stt :str str
+ :lrl (ensure-integer lrl))))
+
+(defun find-ustr-sui (sui &key (srl *current-srl*))
+ "Return the list of ustr for sui"
+ (ensure-sui-integer sui)
+ (collect-umlisp-query (mrcon (cui lui stt str lrl) srl sui sui
+ :lrl lrl)
+ (make-instance 'ustr :sui sui :cui cui :stt stt :str str
+ :cuisui (make-cuisui (ensure-integer cui) sui)
+ :lui (ensure-integer lui) :lrl (ensure-integer lrl))))
+
+(defun find-ustr-sab (sab &key (srl *current-srl*))
+ "Return the list of ustr for sab"
+ (collect-umlisp-query (mrso (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))))))
+
+(defun find-ustr-all (&key (srl *current-srl*))
+ "Return list of all ustr's"
+ (with-sql-connection (db)
+ (clsql:map-query
+ 'list
+ #'(lambda (cui lui sui stt lrl pfstr)
+ (make-instance 'ustr :cui (ensure-integer cui)
+ :lui (ensure-integer lui) :sui (ensure-integer sui)
+ :stt stt :str pfstr
+ :cuisui (make-cuisui (ensure-integer cui)
+ (ensure-integer sui))
+ :lrl (ensure-integer lrl)))
+ (query-string mrcon (cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl
+ :distinct t
+ :order (sui asc))
+ :database db)))
+
+(defun find-string-sui (sui &key (srl *current-srl*))
+ "Return the string associated with sui"
+ (ensure-sui-integer sui)
+ (collect-umlisp-query (mrcon (str) srl sui sui :lrl lrl :single t)
+ str))
+
+(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
+ (ensure-sui-integer sui)
+ (ensure-cui-integer cui)
+ (collect-umlisp-query (mrso (sab code srl tty) srl kcuisui
+ (make-cuisui cui sui) :lrl srl)
+ (make-instance 'uso :sab sab :code code :srl srl :tty tty)))
+
+(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
+ (ensure-cui-integer cui)
+ (ensure-sui-integer sui)
+ (collect-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc)
+ srl kcuisui (make-cuisui cui sui) :lrl ksrl)
+ (make-instance 'ucxt :sab sab :code code
+ :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd
+ :rela rela :xc xc :rnk (ensure-integer rnk)
+ :cui2 (ensure-integer cui2))))
+
+(defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*))
+ (ensure-cui-integer cui)
+ (ensure-lui-integer lui)
+ (ensure-sui-integer sui)
+ (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where "))
+ (cond
+ (sui (string-append ls "KCUISUI='"
+ (integer-string (make-cuisui cui sui) 14)
+ "'"))
+ (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 " 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"
+ (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"
+ (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"
+ (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
+ (find-usty-tui tui)))
+
+(defun find-usab-all ()
+ "Find usab for a key"
+ (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 :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)))
+
+(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)))
+
+(defun find-usab-rsab (rsab)
+ "Find usab for rsab"
+ (find-usab-by-key 'rsab rsab))
+
+(defun find-usab-vsab (vsab)
+ "Find usab for vsab"
+ (find-usab-by-key 'vsab vsab))
+
+(defun find-cui-max ()
+ (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
+
+;;;; Cross table find functions
+
+(defun find-ucon-tui (tui &key (srl *current-srl*))
+ "Find list of ucon for tui"
+ (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
+ :lrl 'klrl :order '(cui asc))
+ (find-ucon-cui cui :srl srl)))
+
+(defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
+ "Return list of ucons that match word, optionally use SQL's LIKE syntax"
+ (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
+ :lrl 'klrl :order '(cui asc))
+ (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"
+ (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"
+ (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 ()
+ (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-uobj-multiword (str obj-lookup-fun sort-fun key srl
+ only-exact-if-match)
+ (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))))
+ (if (and (plusp (length sorted))
+ only-exact-if-match
+ (multiword-match str (pfstr (first sorted))))
+ (first sorted)
+ sorted))))
+
+(defun find-ucon-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
+ #'cui srl only-exact-if-match))
+
+(defun find-uterm-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
+ #'lui srl only-exact-if-match))
+
+(defun find-ustr-multiword (str &key (srl *current-srl*)
+ (only-exact-if-match t))
+ (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
+ #'sui srl only-exact-if-match))
+
+(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))
+
+(defun sort-score-ustr-str (str ustrs)
+ "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
+ (sort-score-umlsclass-str ustrs str #'str))
+
+(defun sort-score-umlsclass-str (objs str lookup-func)
+ "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)))
+ scored))
+ (mapcar #'car (sort scored #'> :key #'cadr))))
+
+
+;;; LEX SQL functions
+
+(defun find-lexterm-eui (eui)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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 wrd
+ :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
+ (ensure-integer eui))))
+
+;;; Semantic Network SQL access functions
+
+(defun find-sdef-ui (ui)
+ (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
+ nil ui ui :single t)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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)
+ (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 4)
+ (insert-ustats-count conn "Concept Count" "MRCON" "distinct CUI" "KCUILRL" srl)
+ (insert-ustats-count conn "Term Count" "MRCON" "distinct KCUILUI" "KCUILRL" srl)
+ (insert-ustats-count conn "Distinct Term Count" "MRCON" "distinct LUI" "KLUILRL" srl)
+ (insert-ustats-count conn "String Count" "MRCON" "*" "LRL" srl)
+ (insert-ustats-count conn "Distinct String Count" "MRCON" "distinct SUI" "LRL" srl)
+ (insert-ustats-count conn "Associated Expression Count" "MRATX" "*" "KSRL" srl)
+ (insert-ustats-count conn "Context Count" "MRCXT" "*" "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 "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)
+ (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
+ (insert-ustats-count conn "Source Count" "MRSO" "*" "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)
+ (insert-ustats-count conn "Bonus Attribute Name Count" "BONUS_ATN" "*" nil srl)
+ (insert-ustats-count conn "Bonus Relationship Count" "BONUS_REL" "*" nil srl)
+ (insert-ustats-count conn "Bonus Source Abbreviation Count" "BONUS_SAB" "*" nil srl)
+ (insert-ustats-count conn "Bonus Term Type Count" "BONUS_TTY" "*" nil 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-orf.git / blobdiff