--- /dev/null
+This is UMLisp - An object-oriented, SQL-based interface library to the
+Unified Medical Language System.
+
+This is open-source software governed by the GNU General Public
+License included with the software in the file COPYING. It is
+Copyright (C) 2000-2002 by Kevin M. Rosenberg.
+
+No documentation is included with this product. Available
+documentation and support options are listed on the UMLisp support web
+site: http://umlisp.med-info.com/support/
+
+
+
--- /dev/null
+;;; $Id: classes.lisp,v 1.1 2002/10/08 22:08:56 kevin Exp $
+;;;
+;;; UMLS object defintions and printing routines
+
+(in-package :umlisp)
+(declaim (optimize (speed 3) (safety 1)))
+
+(defclass umlsclass ()
+ ()
+ (:metaclass ml-class)
+ (:documentation "Parent class of all UMLS objects"))
+
+
+(defmethod print-object ((obj umlsclass) (s stream))
+ (print-unreadable-object (obj s :type t :identity t)
+ (let ((fmt (make-instance 'gu.ml::textformat)))
+ (apply #'format
+ s (funcall (gu.ml::obj-data-fmtstr fmt) obj)
+ (multiple-value-list
+ (funcall (funcall (gu.ml::obj-data-value-func fmt) obj) obj))))))
+
+
+
+
+(defclass urank (umlsclass)
+ ((rank :type fixnum :initarg :rank :reader rank)
+ (sab :type string :initarg :sab :reader sab)
+ (tty :type string :initarg :tty :reader tty)
+ (supres :type string :initarg :supres :reader supres))
+ (:metaclass ml-class)
+ (:default-initargs :rank nil :sab nil :tty nil :supres nil)
+ (:title "Rank")
+ (:fields (rank :fixnum) (sab :string) (tty :string) (supres :string)))
+
+(defclass udef (umlsclass)
+ ((def :type string :initarg :def :reader def)
+ (sab :type string :initarg :sab :reader sab))
+ (:metaclass ml-class)
+ (:default-initargs :def nil :sab nil)
+ (:title "Definition")
+ (:ref-fields (sab find-bsab-sab))
+ (:fields (sab :string) (def :cdata)))
+
+(defclass usat (umlsclass)
+ ((sab :type string :initarg :sab :reader sab)
+ (code :type string :initarg :code :reader code)
+ (atn :type string :initarg :atn :reader atn)
+ (atv :type string :initarg :atv :reader atv))
+ (:metaclass ml-class)
+ (:default-initargs :sab nil :code nil :atn nil :atv nil)
+ (:title "Simple Attribute")
+ (:ref-fields (sab find-bsab-sab))
+ (:fields (sab :string) (code :string) (atn :string) (atv :cdata)))
+
+(defclass uso (umlsclass)
+ ((sab :type string :initarg :sab :reader sab)
+ (code :type string :initarg :code :reader code)
+ (tty :type string :initarg :tty :reader tty)
+ (srl :type fixnum :initarg :srl :reader srl))
+ (:metaclass ml-class)
+ (:default-initargs :sab nil :code nil :tty nil :srl nil)
+ (:title "Source")
+ (:ref-fields (sab find-bsab-sab) (tty find-btty-tty))
+ (:fields (sab :string) (code :string) (tty :string) (srl :fixnum)))
+
+(defclass ucxt (umlsclass)
+ ((sab :type string :initarg :sab :reader sab)
+ (code :type string :initarg :code :reader code)
+ (rnk :type fixnum :initarg :rnk :reader rnk)
+ (cxn :type fixnum :initarg :cxn :reader cxn)
+ (cxl :type string :initarg :cxl :reader cxl)
+ (cxs :type string :initarg :cxs :reader cxs)
+ (cui2 :type fixnum :initarg :cui2 :reader cui2)
+ (hcd :type string :initarg :hcd :reader hcd)
+ (rela :type string :initarg :rela :reader rela)
+ (xc :type string :initarg :xc :reader xc))
+ (:metaclass ml-class)
+ (:default-initargs :sab nil :code nil :rnk nil :cxn nil :cxl nil :cxs nil
+ :cui2 nil :hcd nil :rela nil :xc nil)
+ (:title "Context")
+ (:ref-fields (sab find-bsab-sab) (cui2 find-ucon-cui))
+ (:fields
+ (sab :string) (code :string) (rnk :fixnum) (cxn :fixnum) (cxl :string)
+ (hcd :string) (rela :string) (xc :string) (cui2 :string fmt-cui)
+ (cxs :cdata)))
+
+(defclass ustr (umlsclass)
+ ((sui :type fixnum :initarg :sui :reader sui)
+ (cui :type fixnum :initarg :cui :reader cui)
+ (lui :type fixnum :initarg :lui :reader lui)
+ (cuisui :type integer :initarg :cuisui :reader cuisui )
+ (str :type string :initarg :str :reader str)
+ (lrl :type fixnum :initarg :lrl :reader lrl)
+ (stt :type string :initarg :stt :reader stt)
+ (s#sat :reader s#sat)
+ (s#so :reader s#so)
+ (s#cxt :reader s#cxt))
+ (:metaclass ml-class)
+ (:default-initargs
+ :sui nil :cui nil :lui nil :cuisui nil :str nil :lrl nil :stt nil)
+ (:title "String")
+ (:subobjects-lists (s#sat usat) (s#so uso) (s#cxt ucxt))
+ (:fields (sui :string fmt-sui) (stt :string) (lrl :fixnum) (str :cdata))
+ (:ref-fields (sui find-ustr-sui)))
+
+(defclass ulo (umlsclass)
+ ((isn :type string :initarg :isn :reader isn)
+ (fr :type fixnum :initarg :fr :reader fr)
+ (un :type string :initarg :un :reader un)
+ (sui :type fixnum :initarg :sui :reader sui)
+ (sna :type string :initarg :sna :reader sna)
+ (soui :type string :initarg :soui :reader soui))
+ (:metaclass ml-class)
+ (:default-initargs :isn nil :fr nil :un nil :sui nil :sna nil :soui nil)
+ (:title "Locator")
+ (:fields (isn :string) (fr :fixnum) (un :string) (sna :string)
+ (soui :string) (sui :string fmt-sui) (suistr :string)))
+
+(defclass uterm (umlsclass)
+ ((lui :type fixnum :initarg :lui :reader lui)
+ (cui :type fixnum :initarg :cui :reader cui)
+ (lat :type string :initarg :lat :reader lat)
+ (ts :type string :initarg :ts :reader ts)
+ (lrl :type fixnum :initarg :lrl :reader lrl)
+ (s#str :reader s#str)
+ (s#sat :reader s#sat))
+ (:metaclass ml-class)
+ (:default-initargs :lui nil :cui nil :lat nil :ts nil :lrl nil)
+ (:title "Term")
+ (:subobjects-lists (s#sat usat) (s#str ustr))
+ (:fields (lui :string fmt-lui) (lat :string) (ts :string) (lrl :fixnum))
+ (:ref-fields (lui find-uterm-lui)))
+
+(defclass usty (umlsclass)
+ ((tui :type fixnum :initarg :tui :reader tui)
+ (sty :type string :initarg :sty :reader sty))
+ (:metaclass ml-class)
+ (:default-initargs :tui nil :sty nil)
+ (:title "Semantic Type")
+ (:ref-fields (tui find-ucon-tui (("subobjects" "no"))))
+ (:fields (tui :string fmt-tui) (sty :string)))
+
+(defclass urel (umlsclass)
+ ((rel :type string :initarg :rel :reader rel)
+ (cui1 :type fixnum :initarg :cui1 :reader cui1)
+ (cui2 :type fixnum :initarg :cui2 :reader cui2)
+ (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
+ (rela :type string :initarg :rela :reader rela)
+ (sab :type string :initarg :sab :reader sab)
+ (sl :type string :initarg :sl :reader sl)
+ (mg :type string :initarg :mg :reader mg))
+ (:metaclass ml-class)
+ (:default-initargs
+ :rel nil :cui1 nil :cui2 nil :pfstr2 nil :rela nil :sab nil :sl nil :mg nil)
+ (:title "Relationship")
+ (:ref-fields (rel find-brel-rel) (sab find-bsab-sab) (cui2 find-ucon-cui))
+ (:fields (rel :string) (rela :string) (sab :string) (sl :string)
+ (mg :string) (cui2 :string fmt-cui) (pfstr2 :cdata)))
+
+(defclass ucoc (umlsclass)
+ ((cui1 :type fixnum :initarg :cui1 :reader cui1)
+ (cui2 :type fixnum :initarg :cui2 :reader cui2)
+ (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
+ (soc :type string :initarg :soc :reader soc)
+ (cot :type string :initarg :cot :reader cot)
+ (cof :type fixnum :initarg :cof :reader cof)
+ (coa :type string :initarg :coa :reader coa))
+ (:metaclass ml-class)
+ (:default-initargs
+ :cui1 nil :cui2 nil :pfstr2 nil :soc nil :cot nil :cof nil :coa nil)
+ (:title "Co-occuring Concept")
+ (:ref-fields (cui2 find-ucon-cui))
+ (:fields (soc :string) (cot :string) (cof :fixnum) (coa :cdata)
+ (cui2 :string fmt-cui) (pfstr2 :cdata)))
+
+
+(defclass uatx (umlsclass)
+ ((sab :type string :initarg :sab :reader sab)
+ (rel :type string :initarg :rel :reader rel)
+ (atx :type string :initarg :atx :reader atx))
+ (:metaclass ml-class)
+ (:default-initargs :sab nil :rel nil :atx nil)
+ (:title "Associated Expression")
+ (:fields (sab :string) (rel :string) (atx :cdata)))
+
+(defclass ucon (umlsclass)
+ ((cui :type fixnum :initarg :cui :reader cui )
+ (pfstr :initarg :pfstr :reader pfstr)
+ (lrl :initarg :lrl :reader lrl)
+ (s#term :reader s#term)
+ (s#def :reader s#def)
+ (s#lo :reader s#lo)
+ (s#rel :reader s#rel)
+ (s#coc :reader s#coc)
+ (s#sat :reader s#sat)
+ (s#atx :reader s#atx)
+ (s#sty :reader s#sty))
+ (:metaclass ml-class)
+ (:default-initargs :cui nil :pfstr nil :lrl nil)
+ (:title "Concept")
+ (:subobjects-lists
+ (s#def udef) (s#sty usty) (s#lo ulo) (s#atx uatx) (s#sat usat) (s#rel urel)
+ (s#coc ucoc) (s#term uterm))
+ (:fields (cui :string fmt-cui) (lrl :fixum) (pfstr :cdata))
+ (:ref-fields (cui find-ucon-cui)))
+
+(defclass uxw (umlsclass)
+ ((wd :type string :initarg :wd :reader wd)
+ (cui :type fixnum :initform nil :initarg :cui :reader cui)
+ (lui :type fixnum :initform nil :initarg :lui :reader lui)
+ (sui :type fixnum :initform nil :initarg :sui :reader sui))
+ (:metaclass ml-class)
+ (:default-initargs :wd nil :cui nil :lui nil :sui nil)
+ (:title "XW Index")
+ (:fields (wd :string) (cui :string fmt-cui) (lui :string fmt-lui)
+ (sui :string fmt-sui)))
+
+(defclass uxnw (umlsclass)
+ ((lat :type string :initarg :lat :reader lat)
+ (nwd :type string :initarg :nwd :reader nwd)
+ (cuilist :type list :initarg :cuilist :reader uxnw-cuilist))
+ (:metaclass ml-class)
+ (:default-initargs :lat nil :nwd nil :cuilist nil)
+ (:title "XNW Index")
+ (:fields (lat :string) (nwd :string) (cuilist :string)))
+
+(defclass uxns (umlsclass)
+ ((lat :type string :initarg :lat :reader lat)
+ (nstr :type string :initarg :nstr :reader nstr)
+ (cuilist :type list :initarg :cuilist :reader cuilist))
+ (:metaclass ml-class)
+ (:default-initargs :lat nil :nstr nil :cuilist nil)
+ (:title "XNS Index")
+ (:fields (lat :string) (nstr :string) (cuilist :string)))
+
+
+;;; LEX objects
+
+(defclass lexterm (umlsclass)
+ ((eui :type fixnum :initarg :eui :reader eui)
+ (wrd :type string :initarg :wrd :reader wrd)
+ (s#abr :reader s#abr)
+ (s#agr :reader s#agr)
+ (s#cmp :reader s#cmp)
+ (s#mod :reader s#mod)
+ (s#nom :reader s#nom)
+ (s#prn :reader s#prn)
+ (s#prp :reader s#prp)
+ (s#spl :reader s#spl)
+ (s#trm :reader s#trm)
+ (s#typ :reader s#typ))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :wrd nil)
+ (:title "Lexical Term")
+ (:subobjects-lists
+ (s#abr labr) (s#agr lagr) (s#cmp lcmp) (s#mod lmod) (s#nom unom)
+ (s#prn lprn) (s#prp lprp) (s#spl lspl) (s#trm ltrm) (s#typ ltyp))
+ (:fields (eui :string fmt-eui) (wrd :string))
+ (:ref-fields (eui find-lexterm-eui)))
+
+
+(defclass labr (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (abr :type string :initarg :abr :reader abr)
+ (eui2 :type integer :initarg :eui2 :reader eui2)
+ (bas2 :type string :initarg :bas2 :reader bas2))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :abr nil :eui2 nil :bas2 nil)
+ (:title "Abbreviations and Acronyms")
+ (:fields (eui :string fmt-eui) (bas :string) (abr :string)
+ (eui2 :string fmt-eui) (bas2 :string )))
+
+(defclass lagr (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (str :type string :initarg :str :reader str)
+ (sca :type string :initarg :sca :reader sca)
+ (agr :type string :initarg :agr :reader agr)
+ (cit :type string :initarg :cit :reader cit)
+ (bas :type string :initarg :bas :reader bas))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :str nil :sca nil :agr nil :cit nil :bas nil)
+ (:title "Agreement and Inflection")
+ (:fields (eui :string fmt-eui) (str :string) (sca :string) (agr :string)
+ (cit :string) (bas :string)))
+
+(defclass lcmp (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (sca :type string :initarg :sca :reader sca)
+ (com :type string :initarg :com :reader com))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :sca nil :com nil)
+ (:title "Complementation")
+ (:fields (eui :string fmt-eui) (bas :string) (sca :string) (com :string)))
+
+(defclass lmod (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (sca :type string :initarg :sca :reader sca)
+ (psnmod :type string :initarg :psnmod :reader psnmod)
+ (fea :type string :initarg :fea :reader fea))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :sca nil :psnmod nil :fea nil)
+ (:title "Modifiers")
+ (:fields (eui :string fmt-eui) (bas :string) (sca :string) (psnmod :string)
+ (fea :string)))
+
+(defclass lnom (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (sca :type string :initarg :sca :reader sca)
+ (eui2 :type integer :initarg :eui2 :reader eui2)
+ (bas2 :type string :initarg :bas2 :reader bas2)
+ (sca2 :type string :initarg :sca2 :reader sca2))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :sca nil :eui2 nil :bas2 nil :sca2 nil)
+ (:title "Nominalizations")
+ (:fields (eui :string fmt-eui) (bas :string) (sca :string)
+ (eui2 :string fmt-eui) (bas2 :string) (sca2 :string)))
+
+(defclass lprn (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (num :type string :initarg :num :reader num)
+ (gnd :type string :initarg :gnd :reader gnd)
+ (cas :type string :initarg :cas :reader cas)
+ (pos :type string :initarg :pos :reader pos)
+ (qnt :type string :initarg :qnt :reader qnt)
+ (fea :type string :initarg :fea :reader fea))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :num nil :gnd nil :cas nil
+ :pos nil :qnt nil :fea nil)
+ (:title "Pronouns")
+ (:fields (eui :string fmt-eui) (bas :string) (num :string) (gnd :string)
+ (cas :string) (pos :string) (qnt :string) (fea :string)))
+
+(defclass lprp (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (str :type string :initarg :str :reader str)
+ (sca :type string :initarg :sca :reader sca)
+ (fea :type string :initarg :fea :reader fea))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :str nil :sca nil :fea nil)
+ (:title "Properties")
+ (:fields (eui :string fmt-eui) (bas :string) (str :string) (sca :string)
+ (fea :string)))
+
+
+(defclass lspl (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (spv :type string :initarg :spv :reader spv)
+ (bas :type string :initarg :bas :reader bas))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :spv nil :bas nil)
+ (:title "Spelling Variants")
+ (:fields (eui :string fmt-eui) (spv :string) (bas :string)))
+
+
+
+(defclass ltrm (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (gen :type string :initarg :gen :reader gen))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :gen nil)
+ (:title "Trade Marks")
+ (:fields (eui :string fmt-eui) (bas :string) (gen :string)))
+
+(defclass ltyp (umlsclass)
+ ((eui :type integer :initarg :eui :reader eui)
+ (bas :type string :initarg :bas :reader bas)
+ (sca :type string :initarg :sca :reader sca)
+ (typ :type string :initarg :typ :reader typ))
+ (:metaclass ml-class)
+ (:default-initargs :eui nil :bas nil :sca nil :typ nil)
+ (:title "Inflection Type")
+ (:fields (eui :string fmt-eui) (bas :string) (sca :string) (typ :string)))
+
+(defclass lwd (umlsclass)
+ ((wrd :type string :initarg :wrd :reader wrd)
+ (euilist :type list :initarg :euilist :reader euilist))
+ (:metaclass ml-class)
+ (:default-initargs :wrd nil :euilist nil)
+ (:title "Lexical Word Index")
+ (:fields (wrd :string) (euilist :string)))
+
+;;; Semantic NET objects
+
+(defclass sdef (umlsclass)
+ ((rt :type string :initarg :rt :reader rt)
+ (ui :type integer :initarg :ui :reader ui)
+ (styrl :type string :initarg :styrl :reader styrl)
+ (stnrtn :type string :initarg :stnrtn :reader stnrtn)
+ (def :type string :initarg :def :reader def)
+ (ex :type string :initarg :ex :reader ex)
+ (un :type string :initarg :un :reader un)
+ (rh :type string :initarg :rh :reader rh)
+ (abr :type string :initarg :abr :reader abr)
+ (rin :type string :initarg :rin :reader rin))
+ (:metaclass ml-class)
+ (:default-initargs
+ :rt nil :ui nil :styrl nil :stnrtn nil :def nil :ex nil :un nil :rh nil
+ :abr nil :rin nil)
+ (:title "Basic information about Semantic Types and Relations")
+ (:fields
+ (rt :string) (ui :string fmt-tui) (styrl :string) (stnrtn :string-tui)
+ (def :string) (ex :string) (un :string) (rh :string) (abr :string)
+ (rin :string)))
+
+(defclass sstr (umlsclass)
+ ((styrl :type string :initarg :styrl :reader styrl)
+ (rl :type string :initarg :rl :reader rl)
+ (styrl2 :type string :initarg :styrl2 :reader styrl2)
+ (ls :type string :initarg :ls :reader ls))
+ (:metaclass ml-class)
+ (:default-initargs :styrl nil :rl nil :styrl2 nil :ls nil)
+ (:title "Structure of the Network")
+ (:fields (styrl :string) (rl :string) (styrl2 :string) (ls :string)))
+
+(defclass sstre1 (umlsclass)
+ ((ui :type integer :initarg :ui :reader ui)
+ (ui2 :type integer :initarg :ui2 :reader ui2)
+ (ui3 :type integer :initarg :ui3 :reader ui3))
+ (:metaclass ml-class)
+ (:default-initargs :ui nil :ui2 nil :ui3 nil)
+ (:title "Fully Inherited Set of Releatons (TUI's)")
+ (:fields (ui :string fmt-tui) (ui2 :string fmt-tui) (ui3 :string fmt-tui)))
+
+(defclass sstre2 (umlsclass)
+ ((sty :type string :initarg :ui :reader sty)
+ (rl :type string :initarg :ui2 :reader rl)
+ (sty2 :type string :initarg :ui3 :reader sty2))
+ (:metaclass ml-class)
+ (:default-initargs :sty nil :rl nil :sty2 nil)
+ (:title "Fully Inherited Set of Releatons (strings)")
+ (:fields (sty :string) (rl :string) (sty2 :string)))
+
+;;; Formatting routines
+
+(defmethod fmt-cui ((c ucon))
+ (format nil "C~7,'0d" (cui c)))
+
+(defmethod fmt-cui ((c fixnum))
+ (format nil "C~7,'0d" c))
+
+(defmethod fmt-cui ((c string))
+ (if (eql (aref c 0) #\C)
+ c
+ (format nil "C~7,'0d" (parse-integer c))))
+
+(defmethod fmt-cui ((c null))
+ (format nil "nil"))
+
+(defmethod fmt-lui ((l uterm))
+ (format nil "L~7,'0d" (lui l)))
+
+(defmethod fmt-lui ((l fixnum))
+ (format nil "L~7,'0d" l))
+
+(defmethod fmt-lui ((l string))
+ (if (eql (aref l 0) #\L)
+ l
+ (format nil "L~7,'0d" (parse-integer l))))
+
+(defmethod fmt-sui ((s ustr))
+ (format nil "S~7,'0d" (sui s)))
+
+(defmethod fmt-sui ((s fixnum))
+ (format nil "S~7,'0d" s))
+
+(defmethod fmt-sui ((s string))
+ (if (eql (aref s 0) #\S)
+ s
+ (format nil "S~7,'0d" (parse-integer s))))
+
+(defmethod fmt-tui ((s fixnum))
+ (format nil "T~3,'0d" s))
+
+(defmethod fmt-tui ((s string))
+ (if (eql (aref s 0) #\T)
+ s
+ (format nil "T~3,'0d" (parse-integer s))))
+
+(defmethod fmt-eui ((e fixnum))
+ (format nil "E~7,'0d" e))
+
+(defmethod fmt-eui ((e string))
+ (if (eql (aref e 0) #\E)
+ e
+ (format nil "E~7,'0d" (parse-integer e))))
+
+(defmethod fmt-eui ((e null))
+ (format nil "nil"))
+
+;;; Generic display functions
+
+(eval-when (:compile-toplevel :load-toplevel :execute)
+(defun english-term-p (obj)
+ (and (eq (class-name (class-of obj)) 'uterm)
+ (string-equal (lat obj) "ENG"))))
+
+(defun display-umls-obj
+ (obj &key (os *standard-output*) (format :text) (label nil)
+ (file-wrapper t) (english-only nil) (subobjects nil)
+ (refvars nil))
+ (display-ml-class
+ obj :os os :format format :label label :subobjects subobjects
+ :file-wrapper file-wrapper
+ :english-only-function (if english-only #'english-term-p nil)
+ :refvars refvars))
+
+(defmacro defludisp-ml-class (newfuncname lookup-func)
+ "Defines functions for looking up and displaying objects"
+ `(defun ,newfuncname
+ (keyval &key (os *standard-output*) (format :text) (label nil)
+ (file-wrapper t) (english-only nil) (subobjects nil))
+ (let ((obj (funcall ,lookup-func keyval)))
+ (display-umls-obj obj :os os :format format :label label
+ :file-wrapper file-wrapper :english-only english-only
+ :subobjects subobjects))))
+
+(defludisp-ml-class disp-con #'find-ucon-cui)
+(defludisp-ml-class disp-term #'find-uterm-lui)
+(defludisp-ml-class disp-str #'find-ustr-sui)
+
--- /dev/null
+;;;; $Id: composite.lisp,v 1.1 2002/10/08 22:08:56 kevin Exp $
+
+(in-package :umlisp)
+
+
+;;; Semantic type constants
+
+(defun find-tui-word (words)
+ (gu:aif (car (find-usty-word words))
+ (tui gu::it)
+ nil))
+(gu:memoize 'find-tui-word)
+
+(defun tui-disease-or-syndrome ()
+ (find-tui-word "disease or syndrome"))
+(defun tui-sign-or-symptom ()
+ (find-tui-word "sign or symptom"))
+(defun tui-finding ()
+ (find-tui-word "finding"))
+
+
+;;;; Related concepts with specific tui lookup functions
+
+(defun ucon-is-tui? (ucon tui)
+ "Returns t if ucon has a semantic type of tui"
+ (find tui (s#sty ucon) :key #'tui))
+
+(defun find-ucon2-tui (ucon tui cui2-func related-con-func)
+ "Returns a list of related ucons that have specific tui"
+ (remove-duplicates
+ (filter
+ #'(lambda (c)
+ (gu:aif (funcall cui2-func c)
+ (let ((ucon2 (find-ucon-cui gu::it)))
+ (when (ucon-is-tui? ucon2 tui)
+ ucon2))
+ nil))
+ (funcall related-con-func ucon))
+ :key #'cui))
+
+(defun find-ucon2-coc-tui (ucon tui)
+ "Return list of ucon's that have co-occuring concepts of semantic type tui"
+ (find-ucon2-tui ucon tui #'cui2 #'s#coc))
+
+(defun find-ucon2-rel-tui (ucon tui)
+ "Return list of ucon's that have related concepts to ucon and semantic type tui"
+ (find-ucon2-tui ucon tui #'cui2 #'s#rel))
+
+;;; Composite Objects
+
+(defclass ucon_freq (umlsclass)
+ ((ucon :type ucon :initarg :ucon :reader ucon)
+ (freq :type fixnum :initarg :freq :accessor freq))
+ (:metaclass ml-class)
+ (:default-initargs :cui nil :pfstr nil :freq nil)
+ (:title "Concept and Count")
+ (:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
+ (:ref-fields (cui find-ucon-cui))
+ (:documentation "Composite object of ucon/freq"))
+
+(defun ucon_freq-cui (c)
+ (cui (ucon c)))
+
+(defun ucon_freq-pfstr (c)
+ (pfstr (ucon c)))
+
+(defclass ustr_freq (umlsclass)
+ ((ustr :type ustr :initarg :ustr :reader ustr)
+ (freq :type fixnum :initarg :freq :accessor freq))
+ (:metaclass ml-class)
+ (:default-initargs :cui nil :pfstr nil :freq nil)
+ (:title "String and Count")
+ (:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
+ (:ref-fields (sui find-ustr-sui))
+ (:documentation "Composite object of ustr/freq"))
+
+(defun ustr_freq-sui (s)
+ (sui (ustr s)))
+
+(defun ustr_freq-str (s)
+ (str (ustr s)))
+
+(defun ustr_freq-lrl (s)
+ (lrl (ustr s)))
+
+(defun ustr_freq-stt (s)
+ (stt (ustr s)))
+
+(defclass usty_freq (umlsclass)
+ ((usty :type usty :initarg :usty :reader usty)
+ (freq :type fixnum :initarg :freq :accessor freq))
+ (:metaclass ml-class)
+ (:default-initargs :usty nil :freq nil)
+ (:title "Semantic Type and Count")
+ (:ref-fields (tui find-ucon-tui "subobjects=no"))
+ (:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
+ (:documentation "Composite object of usty/freq"))
+
+(defun usty_freq-tui (s)
+ (tui (usty s)))
+
+(defun usty_freq-sty (s)
+ (sty (usty s)))
+
+(defclass usrl_freq (umlsclass)
+ ((usrl :type usrl :initarg :usrl :reader usrl)
+ (freq :type fixnum :initarg :freq :accessor freq))
+ (:metaclass ml-class)
+ (:default-initargs :usrl nil :freq nil)
+ (:title "Source and Count")
+ (:ref-fields (sab find-ustr-sab))
+ (:fields (sab :string) (freq :commainteger) (srl :fixnum))
+ (:documentation "Composite object of usrl/freq"))
+
+(defun usrl_freq-sab (s)
+ (sab (usrl s)))
+
+(defun usrl_freq-srl (s)
+ (srl (usrl s)))
+
+
+;; Frequency finding functions
+(defun find-ucon2_freq-coc-tui (ucon tui)
+"Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui"
+ (let ((ucon_freqs '()))
+ (dolist (ucoc (s#coc ucon))
+ (gu:aif (cui2 ucoc)
+ (let ((ucon2 (find-ucon-cui gu::it)))
+ (when (ucon-is-tui? ucon2 tui)
+ (push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc))
+ ucon_freqs)))))
+ (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
+ (sort ucon_freqs #'> :key #'freq)))
+
+(defun find-ucon2-str&sty (str sty lookup-func)
+ "Call lookup-func for ucon and usty for given str and sty"
+ (let ((ucon (car (find-ucon-str str)))
+ (usty (car (find-usty-word sty))))
+ (if (and ucon usty)
+ (funcall lookup-func ucon (tui usty))
+ nil)))
+
+(defun find-ucon2-coc-str&sty (str sty)
+ "Find all ucons that are a co-occuring concept for concept named str
+ and that have semantic type of sty"
+ (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))
+
+(defun find-ucon2-rel-str&sty (str sty)
+ "Find all ucons that are a relationship to concept named str
+ and that have semantic type of sty"
+ (find-ucon2-str&sty str sty #'find-ucon2-rel-tui))
+
+;;; Most common relationships, co-occurances
+
+(defun find-ucon2_freq-tui-all (tui ucon2-tui-func)
+ "Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui"
+ (let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
+ (dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
+ (dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
+ (gu:aif (aref ucon_freqs (cui ucon2))
+ (setf (freq gu::it) (1+ (freq gu::it)))
+ (setf (aref ucon_freqs (cui ucon2))
+ (make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
+ (let ((ucon_freq-list '()))
+ (dotimes (i (find-cui-max))
+ (declare (fixnum i))
+ (gu:awhen (aref ucon_freqs i)
+ (push gu::it ucon_freq-list)))
+ (sort ucon_freq-list #'> :key #'freq))))
+
+(defun find-ucon2_freq-rel-tui-all (tui)
+ "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
+ (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))
+
+(defun find-ucon2_freq-coc-tui-all (tui)
+ (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
+
+++ /dev/null
-;;;; $Id: obj-composite.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
-
-(in-package :umlisp)
-
-
-;;; Semantic type constants
-
-(defun find-tui-word (words)
- (gu:aif (car (find-usty-word words))
- (tui gu::it)
- nil))
-(gu:memoize 'find-tui-word)
-
-(defun tui-disease-or-syndrome ()
- (find-tui-word "disease or syndrome"))
-(defun tui-sign-or-symptom ()
- (find-tui-word "sign or symptom"))
-(defun tui-finding ()
- (find-tui-word "finding"))
-
-
-;;;; Related concepts with specific tui lookup functions
-
-(defun ucon-is-tui? (ucon tui)
- "Returns t if ucon has a semantic type of tui"
- (find tui (s#sty ucon) :key #'tui))
-
-(defun find-ucon2-tui (ucon tui cui2-func related-con-func)
- "Returns a list of related ucons that have specific tui"
- (remove-duplicates
- (filter
- #'(lambda (c)
- (gu:aif (funcall cui2-func c)
- (let ((ucon2 (find-ucon-cui gu::it)))
- (when (ucon-is-tui? ucon2 tui)
- ucon2))
- nil))
- (funcall related-con-func ucon))
- :key #'cui))
-
-(defun find-ucon2-coc-tui (ucon tui)
- "Return list of ucon's that have co-occuring concepts of semantic type tui"
- (find-ucon2-tui ucon tui #'cui2 #'s#coc))
-
-(defun find-ucon2-rel-tui (ucon tui)
- "Return list of ucon's that have related concepts to ucon and semantic type tui"
- (find-ucon2-tui ucon tui #'cui2 #'s#rel))
-
-;;; Composite Objects
-
-(defclass ucon_freq (umlsclass)
- ((ucon :type ucon :initarg :ucon :reader ucon)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :cui nil :pfstr nil :freq nil)
- (:title "Concept and Count")
- (:fields (cui :string fmt-cui) (freq :fixnum) (pfstr :cdata))
- (:ref-fields (cui find-ucon-cui))
- (:documentation "Composite object of ucon/freq"))
-
-(defun ucon_freq-cui (c)
- (cui (ucon c)))
-
-(defun ucon_freq-pfstr (c)
- (pfstr (ucon c)))
-
-(defclass ustr_freq (umlsclass)
- ((ustr :type ustr :initarg :ustr :reader ustr)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :cui nil :pfstr nil :freq nil)
- (:title "String and Count")
- (:fields (sui :string fmt-sui) (freq :fixnum) (stt :string) (lrl :fixnum) (str :cdata))
- (:ref-fields (sui find-ustr-sui))
- (:documentation "Composite object of ustr/freq"))
-
-(defun ustr_freq-sui (s)
- (sui (ustr s)))
-
-(defun ustr_freq-str (s)
- (str (ustr s)))
-
-(defun ustr_freq-lrl (s)
- (lrl (ustr s)))
-
-(defun ustr_freq-stt (s)
- (stt (ustr s)))
-
-(defclass usty_freq (umlsclass)
- ((usty :type usty :initarg :usty :reader usty)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :usty nil :freq nil)
- (:title "Semantic Type and Count")
- (:ref-fields (tui find-ucon-tui "subobjects=no"))
- (:fields (tui :string fmt-tui) (freq :fixnum) (sty :string))
- (:documentation "Composite object of usty/freq"))
-
-(defun usty_freq-tui (s)
- (tui (usty s)))
-
-(defun usty_freq-sty (s)
- (sty (usty s)))
-
-(defclass usrl_freq (umlsclass)
- ((usrl :type usrl :initarg :usrl :reader usrl)
- (freq :type fixnum :initarg :freq :accessor freq))
- (:metaclass ml-class)
- (:default-initargs :usrl nil :freq nil)
- (:title "Source and Count")
- (:ref-fields (sab find-ustr-sab))
- (:fields (sab :string) (freq :commainteger) (srl :fixnum))
- (:documentation "Composite object of usrl/freq"))
-
-(defun usrl_freq-sab (s)
- (sab (usrl s)))
-
-(defun usrl_freq-srl (s)
- (srl (usrl s)))
-
-
-;; Frequency finding functions
-(defun find-ucon2_freq-coc-tui (ucon tui)
-"Return sorted list of tuples with ucon and freq that have co-occuring concepts of semantic type tui"
- (let ((ucon_freqs '()))
- (dolist (ucoc (s#coc ucon))
- (gu:aif (cui2 ucoc)
- (let ((ucon2 (find-ucon-cui gu::it)))
- (when (ucon-is-tui? ucon2 tui)
- (push (make-instance 'ucon_freq :ucon ucon2 :freq (cof ucoc))
- ucon_freqs)))))
- (setq ucon_freqs (delete-duplicates ucon_freqs :key #'cui))
- (sort ucon_freqs #'> :key #'freq)))
-
-(defun find-ucon2-str&sty (str sty lookup-func)
- "Call lookup-func for ucon and usty for given str and sty"
- (let ((ucon (car (find-ucon-str str)))
- (usty (car (find-usty-word sty))))
- (if (and ucon usty)
- (funcall lookup-func ucon (tui usty))
- nil)))
-
-(defun find-ucon2-coc-str&sty (str sty)
- "Find all ucons that are a co-occuring concept for concept named str
- and that have semantic type of sty"
- (find-ucon2-str&sty str sty #'find-ucon2-coc-tui))
-
-(defun find-ucon2-rel-str&sty (str sty)
- "Find all ucons that are a relationship to concept named str
- and that have semantic type of sty"
- (find-ucon2-str&sty str sty #'find-ucon2-rel-tui))
-
-;;; Most common relationships, co-occurances
-
-(defun find-ucon2_freq-tui-all (tui ucon2-tui-func)
- "Return sorted list of all ucon2 that have a semantic type tui with ucon that is also has sty of tui"
- (let ((ucon_freqs (make-array (1+ (find-cui-max)) :initial-element nil)))
- (dolist (ucon (find-ucon-tui tui)) ;; for all disease-or-syn
- (dolist (ucon2 (funcall ucon2-tui-func ucon tui)) ;; for each related disease
- (gu:aif (aref ucon_freqs (cui ucon2))
- (setf (freq gu::it) (1+ (freq gu::it)))
- (setf (aref ucon_freqs (cui ucon2))
- (make-instance 'ucon_freq :ucon ucon2 :freq 1)))))
- (let ((ucon_freq-list '()))
- (dotimes (i (find-cui-max))
- (declare (fixnum i))
- (gu:awhen (aref ucon_freqs i)
- (push gu::it ucon_freq-list)))
- (sort ucon_freq-list #'> :key #'freq))))
-
-(defun find-ucon2_freq-rel-tui-all (tui)
- "Sorted list of ucon_freq with semantic type tui that are rel's of ucons with semantic type tui"
- (find-ucon2_freq-tui-all tui #'find-ucon2-rel-tui))
-
-(defun find-ucon2_freq-coc-tui-all (tui)
- (find-ucon2_freq-tui-all tui #'find-ucon2-coc-tui))
-
+++ /dev/null
-;;; $Id: obj-sql.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
-
-(in-package :umlisp)
-
-(declaim (optimize (speed 3) (safety 1)))
-
-(defvar *current-srl* nil)
-(defun current-srl ()
- *current-srl*)
-(defun current-srl! (srl)
- (setq *current-srl* srl))
-
-;;; Initializers
-
-(defun post-import-sql ()
- (make-ustats)
- (make-usrl)
- (make-user-table)
- #+pubmed (create-pmsearch-table))
-
-;;; Accessors (read on demand)
-
-;; defines a slot-unbound method for class and slot-name, fills
-;; the slot by calling reader function with the slot values of
-;; the instance's reader-keys
-(defmacro def-lazy-reader (class slot-name reader &rest reader-keys)
- (let* ((the-slot-name (gensym))
- (the-class (gensym))
- (the-instance (gensym))
- (keys '()))
- (dolist (key reader-keys)
- (push (list 'slot-value the-instance (list 'quote key)) keys))
- (setq keys (nreverse keys))
- `(defmethod slot-unbound (,the-class (,the-instance ,class)
- (,the-slot-name (eql ',slot-name)))
- (declare (ignore ,the-class))
- (setf (slot-value ,the-instance ,the-slot-name)
- (,reader ,@keys)))))
-
-(def-lazy-reader ucon s#term find-uterm-cui cui)
-(def-lazy-reader ucon s#def find-udef-cui cui)
-(def-lazy-reader ucon s#sty find-usty-cui cui)
-(def-lazy-reader ucon s#rel find-urel-cui cui)
-(def-lazy-reader ucon s#coc find-ucoc-cui cui)
-(def-lazy-reader ucon s#lo find-ulo-cui cui)
-(def-lazy-reader ucon s#atx find-uatx-cui cui)
-(def-lazy-reader ucon s#sat find-usat-ui cui)
-
-;; For uterms
-(def-lazy-reader uterm s#str find-ustr-cuilui cui lui)
-(def-lazy-reader uterm s#sat find-usat-ui cui lui)
-
-;; For ustrs
-(def-lazy-reader ustr s#sat find-usat-ui cui lui sui)
-(def-lazy-reader ustr s#cxt find-ucxt-cuisui cui sui)
-(def-lazy-reader ustr s#so find-uso-cuisui cui sui)
-
-;;; Object lookups
-
-;;; Lookup functions for uterms,ustr in ucons
-
-(defun find-uterm-in-ucon (ucon lui)
- (find lui (s#term ucon) :key #'uterm-lui :test 'equal))
-
-(defun find-ustr-in-uterm (uterm sui)
- (find sui (s#str uterm) :key #'ustr-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))
-
-
-(defun find-ucon-cui (cui &key (srl *current-srl*))
- "Find ucon for a cui"
- (if (stringp cui)
- (setq cui (parse-cui cui)))
- (if cui
- (let ((ls (format nil "select KPFSTR,KCUILRL from MRCON where CUI=~d"
- cui)))
- (if srl
- (string-append ls (format nil " and KCUILRL <= ~d limit 1" srl))
- (string-append ls " limit 1"))
- (gu:awhen (car (mutex-sql-query ls))
- (make-instance 'ucon :cui cui :pfstr (car gu::it)
- :lrl (ensure-integer (cadr gu::it)))))
- nil))
-
-(defun find-ucon-lui (lui &key (srl *current-srl*))
- "Find list of ucon for lui"
- (if (stringp lui)
- (setq lui (parse-lui lui)))
- (if lui
- (let ((ucons '())
- (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where LUI=~d" lui)))
- (if srl
- (string-append ls (format nil " and KCUILRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
- :pfstr (nth 1 tuple)
- :lrl (ensure-integer (nth 2 tuple)))
- ucons))
- (nreverse ucons))
- nil))
-
-(defun find-ucon-sui (sui &key (srl *current-srl*))
- "Find list of ucon for sui"
- (if (stringp sui)
- (setq sui (parse-sui sui)))
- (if sui
- (let ((ucons '())
- (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where SUI=~d" sui)))
- (when srl
- (string-append ls (format nil " and KCUILRL <= ~d" srl)))
- (let ((tuples (mutex-sql-query ls)))
- (dolist (tuple tuples)
- (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
- :pfstr (nth 1 tuple)
- :lrl (ensure-integer (nth 2 tuple)))
- ucons)))
- (nreverse ucons))
- nil))
-
-(defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
- "Find ucon for cui/sui"
- (if (stringp cui)
- (setq cui (parse-cui cui)))
- (if (stringp sui)
- (setq sui (parse-sui sui)))
- (if (and cui sui)
- (let ((ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where KCUISUI=~d"
- (make-cuisui cui sui))))
- (when srl
- (string-append ls (format nil " and KCUILRL <= ~d" srl)))
- (gu:aif (car (mutex-sql-query ls))
- (make-instance 'ucon :cui (ensure-integer (nth 0 gu::it))
- :pfstr (nth 1 gu::it)
- :lrl (ensure-integer (nth 2 gu::it)))
- nil))
- nil))
-
-(defun find-ucon-str (str &key (srl *current-srl*))
- "Find ucon that are exact match for str"
- (if str
- (let ((ucons '())
- (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where STR='~a'" str)))
- (when srl
- (string-append ls " and KCUILRL <= ~d" srl))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
- :pfstr (nth 1 tuple)
- :lrl (ensure-integer (nth 2 tuple))) ucons))
- (nreverse ucons))
- nil))
-
-(defun find-ucon-all (&key (srl *current-srl*))
- "Return list of all ucon's"
- (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
- (when srl
- (string-append ls (format nil " where KCUILRL <= ~d" srl)))
- (string-append ls " order by CUI asc")
- (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)))
- ls
- :database db))))
-
-
-
-(defun find-udef-cui (cui &key (srl *current-srl*))
- "Return a list of udefs for cui"
- (let ((udefs '())
- (ls (format nil "select SAB,DEF from MRDEF where CUI=~d" cui)))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'udef :sab (car tuple) :def (cadr tuple)) udefs))
- (nreverse udefs)))
-
-(defun find-usty-cui (cui &key (srl *current-srl*))
- "Return a list of usty for cui"
- (let ((ustys '())
- (ls (format nil "select TUI,STY from MRSTY where CUI=~d" cui)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
- ustys))
-
-(defun find-usty-word (word &key (srl *current-srl*))
- "Return a list of usty that match word"
- (let ((ustys '())
- (ls (format nil "select distinct TUI,STY from MRSTY where STY like '%~a%'" word)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
- ustys))
-
-(defun find-urel-cui (cui &key (srl *current-srl*))
- "Return a list of urel for cui"
- (let ((urels '())
- (ls (format nil "select REL,CUI2,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI1=~d" cui)))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'urel
- :cui1 cui
- :rel (nth 0 tuple)
- :cui2 (ensure-integer (nth 1 tuple))
- :rela (nth 2 tuple)
- :sab (nth 3 tuple)
- :sl (nth 4 tuple)
- :mg (nth 5 tuple)
- :pfstr2 (nth 6 tuple))
- urels))
- (nreverse urels)))
-
-(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
- "Return a list of urel for cui2"
- (let ((urels '())
- (ls (format nil "select REL,CUI1,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI2=~d" cui2)))
- (when srl
- (string-append ls (format nil " and SRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'urel
- :cui2 cui2
- :rel (nth 0 tuple)
- :cui1 (ensure-integer (nth 1 tuple))
- :rela (nth 2 tuple)
- :sab (nth 3 tuple)
- :sl (nth 4 tuple)
- :mg (nth 5 tuple)
- :pfstr2 (nth 6 tuple))
- urels))
- (nreverse urels)))
-
-(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
- (mapcar
- #'(lambda (cui) (find-ucon-cui cui :key srl))
- (remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))))
-
-(defun find-ucoc-cui (cui &key (srl *current-srl*))
- "Return a list of ucoc for cui"
- (let ((ucocs '())
- (ls (format nil "select CUI2,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI1=~d" cui)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (string-append ls " order by COF asc")
- (dolist (tuple (mutex-sql-query ls))
- (let ((cui2 (ensure-integer (nth 0 tuple))))
- (when (zerop cui2)
- (setq cui2 nil))
- (push (make-instance 'ucoc :cui1 cui
- :cui2 cui2
- :soc (nth 1 tuple)
- :cot (nth 2 tuple)
- :cof (ensure-integer (nth 3 tuple))
- :coa (nth 4 tuple)
- :pfstr2 (nth 5 tuple))
- ucocs)))
- ucocs)) ;; akready ordered by SQL select
-
-(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
- "Return a list of ucoc for cui2"
- (let ((ucocs '())
- (ls (format nil "select CUI1,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI2=~d" cui2)))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (string-append ls " order by COF asc")
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ucoc :cui1 (ensure-integer (nth 0 tuple))
- :cui2 cui2
- :soc (nth 1 tuple)
- :cot (nth 2 tuple)
- :cof (ensure-integer (nth 3 tuple))
- :coa (nth 4 tuple)
- :pfstr2 (nth 5 tuple))
- ucocs))
- ucocs)) ;; already ordered by SQL select
-
-(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
- "List of ucon with co-occurance cui2"
- (mapcar
- #'(lambda (cui) (find-ucon-cui cui :key 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"
- (let ((ulos '())
- (ls (format nil "select ISN,FR,UN,SUI,SNA,SOUI from MRLO where CUI=~d" cui)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ulo :isn (nth 0 tuple)
- :fr (ensure-integer (nth 1 tuple))
- :un (nth 2 tuple)
- :sui (ensure-integer (nth 3 tuple))
- :sna (nth 4 tuple)
- :soui (nth 5 tuple))
- ulos))
- (nreverse ulos)))
-
-(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"
- (let ((uatxs '())
- (ls (format nil "select SAB,REL,ATX from MRATX where CUI=~d" cui)))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'uatx :sab (nth 0 tuple)
- :rel (nth 1 tuple)
- :atx (nth 2 tuple))
- uatxs))
- (nreverse uatxs)))
-
-
-(defun find-uterm-cui (cui &key (srl *current-srl*))
- "Return a list of uterm for cui"
- (let ((uterms '())
- (ls (format nil "select distinct LUI,LAT,TS,KLUILRL from MRCON where CUI=~d" cui)))
- (when srl
- (string-append ls (format nil " and KLUILRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'uterm :lui (ensure-integer (nth 0 tuple))
- :cui cui
- :lat (nth 1 tuple)
- :ts (nth 2 tuple)
- :lrl (ensure-integer (nth 3 tuple)))
- uterms))
- (nreverse uterms)))
-
-(defun find-uterm-lui (lui &key (srl *current-srl*))
- "Return a list of uterm for lui"
- (if (stringp lui)
- (setq lui (parse-lui lui)))
- (let ((uterms '())
- (ls (format nil "select distinct CUI,LAT,TS,KLUILRL from MRCON where LUI=~d" lui)))
- (when srl
- (string-append ls (format nil " and KLUILRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'uterm :cui (ensure-integer (nth 0 tuple))
- :lui lui
- :lat (nth 1 tuple)
- :ts (nth 2 tuple)
- :lrl (ensure-integer (nth 3 tuple)))
- uterms))
- (nreverse uterms)))
-
-(defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
- "Return single uterm for cui/lui"
- (let ((ls (format nil "select LAT,TS,KLUILRL from MRCON where KCUILUI=~d limit 1" (make-cuilui cui lui))))
- (when srl
- (string-append ls (format nil " and KLUILRL <= ~d" srl)))
- (gu:aif (car (mutex-sql-query ls))
- (make-instance 'uterm :cui cui
- :lui lui
- :lat (nth 0 gu::it)
- :ts (nth 1 gu::it)
- :lrl (ensure-integer (nth 2 gu::it)))
- nil)))
-
-(defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
- "Return a list of ustr for cui/lui"
- (declare (fixnum cui lui))
- (let ((ustrs '())
- (ls (format nil "select SUI,STT,STR,LRL from MRCON where KCUILUI=~d" (make-cuilui cui lui))))
- (when srl
- (string-append ls (format nil " and LRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (let* ((sui (ensure-integer (car tuple)))
- (ustr (make-instance 'ustr :sui sui
- :cui cui
- :cuisui (make-cuisui cui sui)
- :lui lui
- :stt (nth 1 tuple)
- :str (nth 2 tuple)
- :lrl (ensure-integer (nth 3 tuple)))))
- (push ustr ustrs)))
- (nreverse ustrs)))
-
-(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
- "Return the single ustr for cuisui"
- (let ((ls (format nil "select LUI,STT,STR,LRL from MRCON where KCUISUI=~d"
- (make-cuisui cui sui))))
- (when srl
- (string-append ls (format nil " and LRL <= ~d" srl)))
- (gu:aif (car (mutex-sql-query ls))
- (make-instance 'ustr :sui sui
- :cui cui
- :cuisui (make-cuisui cui sui)
- :lui (ensure-integer (nth 0 gu::it))
- :stt (nth 1 gu::it)
- :str (nth 2 gu::it)
- :lrl (ensure-integer (nth 3 gu::it)))
- nil)))
-
-(defun find-ustr-sui (sui &key (srl *current-srl*))
- "Return the list of ustr for sui"
- (if (stringp sui)
- (setq sui (parse-sui sui)))
- (let ((ustrs '())
- (ls (format nil "select CUI,LUI,STT,STR,LRL from MRCON where SUI=~d" sui)))
- (when srl
- (string-append ls (format nil " and LRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (let ((cui (ensure-integer (car tuple))))
- (push (make-instance 'ustr :sui sui
- :cui cui
- :cuisui (make-cuisui cui sui)
- :lui (ensure-integer (nth 1 tuple))
- :stt (nth 2 tuple)
- :str (nth 3 tuple)
- :lrl (ensure-integer (nth 4 tuple)))
- ustrs)))
- (nreverse ustrs)))
-
-(defun find-ustr-sab (sab &key (srl *current-srl*))
- "Return the list of ustr for sab"
- (let ((ustrs '())
- (ls (format nil "select KCUISUI from MRSO where SAB='~a'" sab)))
- (when srl
- (string-append ls (format nil " and SRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (let ((cuisui (ensure-integer (car tuple))))
- (push (apply #'find-ustr-cuisui
- (append
- (multiple-value-list (decompose-cuisui cuisui))
- (list :srl srl)))
- ustrs)))
- (nreverse ustrs)))
-
-(defun find-ustr-all (&key (srl *current-srl*))
- "Return list of all ustr's"
- (let ((ls "select distinct CUI,LUI,SUI,STT,LRL,KPFSTR from MRCON"))
- (when srl
- (string-append ls (format nil " where LRL <= ~d" srl)))
- (string-append ls " order by SUI asc")
- (with-sql-connection (db)
- (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))
- ls
- :database db))))
-
-(defun find-string-sui (sui &key (srl *current-srl*))
- "Return the string associated with sui"
- (let ((ls (format nil "select STR from MRCON where SUI=~d" sui)))
- (when srl
- (string-append ls (format nil " and LRL <= ~d" srl)))
- (string-append ls " limit 1")
- (caar (mutex-sql-query ls))))
-
-(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
- (declare (fixnum cui sui))
- (let ((usos '())
- (ls (format nil "select SAB,CODE,SRL,TTY from MRSO where KCUISUI=~d"
- (make-cuisui cui sui))))
- (when srl
- (string-append ls (format nil " and SRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'uso :sab (nth 0 tuple) :code (nth 1 tuple)
- :srl (nth 2 tuple) :tty (nth 3 tuple))
- usos))
- (nreverse usos)))
-
-(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
- (declare (fixnum cui sui))
- (let ((ucxts '())
- (ls (format nil "select SAB,CODE,CXN,CXL,RNK,CXS,CUI2,HCD,RELA,XC from MRCXT where KCUISUI=~d"
- (make-cuisui cui sui))))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ucxt :sab (nth 0 tuple)
- :code (nth 1 tuple)
- :cxn (ensure-integer (nth 2 tuple))
- :cxl (nth 3 tuple)
- :rnk (ensure-integer (nth 4 tuple))
- :cxs (nth 5 tuple)
- :cui2 (ensure-integer (nth 6 tuple))
- :hcd (nth 7 tuple)
- :rela (nth 8 tuple)
- :xc (nth 9 tuple))
- ucxts))
- (nreverse ucxts)))
-
-(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 ")))
- (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))))
- (when srl
- (string-append ls (format nil " and KSRL <= ~d" srl)))
- (let ((usats '()))
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'usat :code (nth 0 tuple)
- :atn (nth 1 tuple)
- :sab (nth 2 tuple)
- :atv (nth 3 tuple))
- usats))
- (nreverse usats))))
-
-(defun find-bsab-sab (sab)
- (gu:aif (car (mutex-sql-query
- (format nil "select NAME,COUNT from BONUS_SAB where SAB='~a'" sab)))
- (make-instance 'bsab :sab sab :name (nth 0 gu::it)
- :hits (ensure-integer (nth 1 gu::it)))
- nil))
-
-(defun find-bsab-all ()
- (let ((usabs '()))
- (dolist (tuple (mutex-sql-query "select SAB,NAME,COUNT from BONUS_SAB"))
- (push
- (make-instance 'bsab :sab (nth 0 tuple) :name (nth 1 tuple)
- :hits (ensure-integer (nth 2 tuple)))
- usabs))
- (nreverse usabs)))
-
-(defun find-btty-tty (tty)
- (gu:aif (car (mutex-sql-query
- (format nil "select NAME from BONUS_TTY where TTY='~a'" tty)))
- (make-instance 'btty :tty tty :name (nth 0 gu::it))
- nil))
-
-(defun find-btty-all ()
- (let ((uttys '()))
- (dolist (tuple (mutex-sql-query "select TTY,NAME from BONUS_TTY"))
- (push
- (make-instance 'btty :tty (nth 0 tuple) :name (nth 1 tuple))
- uttys))
- (nreverse uttys)))
-
-(defun find-brel-rel (rel)
- (let ((brels '()))
- (dolist (tuple (mutex-sql-query
- (format nil "select SAB,SL,REL,RELA,COUNT from BONUS_REL where REL='~a'" rel)))
- (push
- (make-instance 'brel :sab (nth 0 tuple) :sl (nth 1 tuple) :rel (nth 2 tuple)
- :rela (nth 3 tuple) :hits (ensure-integer (nth 4 tuple)))
- brels))
- (nreverse brels)))
-
-(defun find-pfstr-cui (cui)
- (caar (mutex-sql-query (format nil "select KPFSTR from MRCON where CUI=~d limit 1" cui))))
-
-(defun find-usty-tui (tui)
- "Find usty for tui"
- (setq tui (parse-tui tui))
- (gu:aif (car (mutex-sql-query
- (format nil "select STY from MRSTY where TUI=~d limit 1" tui)))
- (make-instance 'usty :tui tui :sty (nth 0 gu::it))
- nil))
-
-(defun find-usty-sty (sty)
- "Find usty for a sty"
- (gu:aif (car (mutex-sql-query
- (format nil "select TUI from MRSTY where STY='~a' limit 1" sty)))
- (make-instance 'usty :tui (ensure-integer (nth 0 gu::it)) :sty sty)
- nil))
-
-(defun find-usty-all ()
- "Return list of usty's for all semantic types"
- (let ((ustys '()))
- (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
- (push (find-usty-tui (nth 0 tuple)) ustys))
- (nreverse ustys)))
-
-(defun find-usty_freq-all ()
- (let ((usty_freqs '()))
- (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
- (let* ((tui (car tuple))
- (freq (ensure-integer
- (caar (mutex-sql-query
- (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
- (push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
- (sort usty_freqs #'> :key #'usty_freq-freq)))
-
-
-(defun make-user-table ()
- (mutex-sql-execute "create table UMLISP_USERS (ID integer UNSIGNED NOT NULL AUTO_INCREMENT PRIMARY KEY,FIRST_NAME varchar(20),LAST_NAME varchar(20),ORGANIZATION varchar(80),ADDRESS1 varchar(60),ADDRESS2 varchar(60),CITY varchar(30),STATE char(2),ZIP char(10),COUNTRY varchar(40),OCCUPATION varchar(120),EMAIL varchar(80),PASSWD varchar(20),MAILLIST char(1),LICENSED char(1),SRL integer,TIMEOUT integer,DATETIME_CREATED datetime,DATETIME_MODIFIED datetime)"))
-
-(defun find-umlisp-user-email (email)
- (let ((tuple (car (mutex-sql-query
- (format nil "select ID,FIRST_NAME,LAST_NAME,ORGANIZATION,ADDRESS1,ADDRESS2,CITY,STATE,ZIP,COUNTRY,OCCUPATION,LICENSED,MAILLIST,PASSWD,SRL,TIMEOUT,DATETIME_CREATED,DATETIME_MODIFIED from UMLISP_USERS where EMAIL='~a'" email)))))
- (when tuple
- (make-instance 'umlisp-user :email email
- :id (ensure-integer (nth 0 tuple))
- :first-name (nth 1 tuple)
- :last-name (nth 2 tuple)
- :organization (nth 3 tuple)
- :address1 (nth 4 tuple)
- :address2 (nth 5 tuple)
- :city (nth 6 tuple)
- :state (nth 7 tuple)
- :zip (nth 8 tuple)
- :country (nth 9 tuple)
- :occupation (nth 10 tuple)
- :licensed (if (string-equal "Y" (nth 11 tuple)) t nil)
- :maillist (if (string-equal "Y" (nth 12 tuple)) t nil)
- :passwd (nth 13 tuple)
- :srl (ensure-integer (nth 14 tuple))
- :timeout (ensure-integer (nth 15 tuple))
- :datetime-created (nth 16 tuple)
- :datetime-modified (nth 17 tuple)))))
-
-(defun find-umlisp-user-all ()
- (let ((users '()))
- (dolist (email (find-umlisp-user-all-email))
- (push (find-umlisp-user-email email) users))
- (nreverse users)))
-
-(defun find-umlisp-user-all-email ()
- (let ((emails '()))
- (dolist (tuple (mutex-sql-query "select EMAIL from UMLISP_USERS"))
- (push (car tuple) emails))
- (nreverse emails)))
-
-(defun find-umlisp-user-announce-email ()
- (let ((emails '()))
- (dolist (tuple (mutex-sql-query
- "select EMAIL from UMLISP_USERS where MAILLIST='Y'"))
- (push (car tuple) emails))
- (nreverse emails)))
-
-(defun add-umlisp-user (user)
- (if (typep user 'umlisp-user)
- (progn
- (mutex-sql-execute
- (format nil "insert into UMLISP_USERS (FIRST_NAME,LAST_NAME,ORGANIZATION,ADDRESS1,ADDRESS2,CITY,STATE,ZIP,COUNTRY,OCCUPATION,LICENSED,MAILLIST,EMAIL,PASSWD,SRL,TIMEOUT,DATETIME_CREATED,DATETIME_MODIFIED) values ('~a','~a','~a','~a','~a','~a','~a','~a','~a','~a','~a','~a','~a','~a',~d,~d,NOW(),NOW())"
- (first-name user) (last-name user)
- (organization user)
- (address1 user) (address2 user)
- (city user) (state user)
- (zip user) (country user) (occupation user)
- (if (licensed user) #\Y #\N)
- (if (maillist user) #\Y #\N)
- (email user)
- (passwd user) (srl user)
- (timeout user)))
- (let ((read-user (find-umlisp-user-email (email user))))
- (setf (slot-value user 'id) (id read-user)
- (slot-value user 'datetime-created) (datetime-created read-user)
- (slot-value user 'datetime-modified) (datetime-modified read-user)))
- t)
- nil))
-
-(defun umlisp-user-verify-passwd (user passwd)
- (when user
- (string-equal passwd (passwd user))))
-
-(defun umlisp-user-set-srl (email srl)
- (when (and (integerp srl) (find-umlisp-user-email email))
- (mutex-sql-execute
- (format nil "update UMLISP_USERS set SRL=~d,DATETIME_MODIFIED=NOW() where EMAIL='~a'" srl email))
- srl))
-
-(defun make-ustats ()
- (with-sql-connection (conn)
- (sql-execute "drop table if exists 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*))
- (let ((ustats '())
- (ls "select NAME,COUNT,SRL from USTATS"))
- (when srl
- (string-append ls (format nil " where SRL=~d" srl)))
- (string-append ls " order by NAME asc")
- (dolist (tuple (mutex-sql-query ls))
- (push (make-instance 'ustats :name (nth 0 tuple)
- :hits (ensure-integer (nth 1 tuple))
- :srl (ensure-integer (nth 2 tuple)))
- ustats))
- (nreverse ustats)))
-
-(defun find-ustats-srl (srl)
- (let ((ustats '()))
- (dolist (tuple (mutex-sql-query
- (format nil "select NAME,COUNT from USTATS where SRL=~d order by NAME asc" srl)))
- (push (make-instance 'ustats :name (nth 0 tuple)
- :hits (ensure-integer (nth 1 tuple))
- :srl srl)
- ustats))
- (nreverse ustats)))
-
-(defun make-usrl ()
- (with-sql-connection (conn)
- (sql-execute "drop table if exists USRL" conn)
- (sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
- (dolist (tuple (mutex-sql-query "select distinct SAB,SRL from MRSO order by SAB asc"))
- (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
- (car tuple) (ensure-integer (cadr tuple)))
- conn)))
- (find-usrl-all))
-
-(defun find-usrl-all ()
- (let ((usrls '())
- (tuples (mutex-sql-query "select SAB,SRL from USRL order by SAB desc")))
- (dolist (tuple tuples)
- (push (make-instance 'usrl :sab (nth 0 tuple)
- :srl (ensure-integer (nth 1 tuple))) usrls))
- usrls)) ;; already reversed by sql
-
-(defun find-usrl_freq-all ()
- (let ((freqs '()))
- (dolist (usrl (find-usrl-all))
- (let ((freq (ensure-integer
- (caar (mutex-sql-query
- (format nil "select count(*) from MRSO where SAB='~a'"
- (sab usrl)))))))
- (push (make-instance 'usrl_freq :usrl usrl :freq freq) freqs)))
- (sort freqs #'> :key #'usrl_freq-freq)))
-
-(defun find-cui-max ()
- (let ((cui (caar (mutex-sql-query "select max(CUI) from MRCON"))))
- (ensure-integer cui)))
-
-;;;; Cross table find functions
-
-(defun find-ucon-tui (tui &key (srl *current-srl*))
- "Find list of ucon for tui"
- (when (stringp tui)
- (setq tui (parse-tui tui)))
- (let ((ucons '())
- (ls (format nil "select CUI from MRSTY where TUI=~d" tui)))
- (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 (ensure-integer (car tuple)) :srl srl) ucons))
- ucons))
-
-(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))
-
-(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))
-
-(defun find-ustr-word (word &key (srl *current-srl*))
- "Return list of ustrs that match word"
- (let ((ustrs '())
- (ls (format nil "select cui,sui from MRXW_ENG where wd='~a'" word)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (string-append ls " order by cui desc,sui desc")
- (dolist (tuple (mutex-sql-query ls))
- (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
- ustrs))
- ustrs))
-
-(defun find-ustr-normalized-word (word &key (srl *current-srl*))
- "Return list of ustrs that match word"
- (let ((ustrs '())
- (ls (format nil "select cui,sui from MRXNW_ENG where nwd='~a'" word)))
- (when srl
- (string-append ls (format nil " and KLRL <= ~d" srl)))
- (string-append ls " order by cui desc,sui desc")
- (dolist (tuple (mutex-sql-query ls))
- (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
- ustrs))
- ustrs))
-
-
-;;; 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-ucon-normalized-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 '())
- (nwords '()))
- (dolist (word words)
- (let ((nws (lvg:process-terms word)))
- (dolist (nword nws)
- (push nword nwords))))
- (dolist (word nwords)
- (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 find-ustr-normalized-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 '())
- (nwords '()))
- (dolist (word words)
- (let ((nws (lvg:process-terms word)))
- (dolist (nword nws)
- (push nword nwords))))
- (dolist (word nwords)
- (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
- (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'ustr-cui))))
-
-(defun a (str)
- (find-normalized-matches-for-str str #'find-ustr-normalized-word #'ustr-sui))
-
-(defun find-normalized-matches-for-str (str lookup-func key-func)
- "Return list of objects that normalize match for words in string,
-eliminate duplicates."
- (let ((objs '())
- (nwords '()))
- (dolist (word (delimited-string-to-list str #\space))
- (dolist (nword (lvg:process-terms word))
- (unless (member nword nwords :test #'string-equal)
- (push nword nwords))))
- (dolist (nw nwords)
- (setq objs (append objs (funcall lookup-func nw))))
- (delete-duplicates objs :key key-func :test #'eql)))
-
-(defun sort-score-ucon-str (str ucons)
- "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
- (sort-score-umlsclass-str ucons 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))))
-
-(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))
- (gu:aif (position (nth iword short-list) long-list :test #'string-equal)
- (progn
- (incf score (- 10 (abs (- gu::it iword))))
- (decf unmatched))))
- (decf score (* 2 unmatched))
- score))
-
-
-;;; LEX SQL functions
-
-(defun find-lexterm-eui (eui)
- (gu:awhen (car (mutex-sql-query
- (format nil "select WRD from LRWD where EUI=~d" eui)))
- (make-instance 'lexterm :eui eui :wrd (nth 0 gu:it))))
-
-(defun find-lexterm-word (wrd)
- (gu:awhen (mutex-sql-query
- (format nil "select EUI from LRWD where WRD='~a'" wrd))
- (let ((terms '()))
- (dolist (tuple gu:it)
- (let ((eui (ensure-integer (nth 0 tuple))))
- (push
- (make-instance 'lexterm :eui eui :wrd (copy-seq wrd))
- terms)))
- (nreverse terms))))
-
-;; LEXTERM accessors, read on demand
-
-(def-lazy-reader lexterm s#abr find-labr-eui eui)
-(def-lazy-reader lexterm s#agr find-lagr-eui eui)
-(def-lazy-reader lexterm s#cmp find-lcmp-eui eui)
-(def-lazy-reader lexterm s#mod find-lmod-eui eui)
-(def-lazy-reader lexterm s#nom find-lnom-eui eui)
-(def-lazy-reader lexterm s#prn find-lprn-eui eui)
-(def-lazy-reader lexterm s#prp find-lprp-eui eui)
-(def-lazy-reader lexterm s#spl find-lspl-eui eui)
-(def-lazy-reader lexterm s#trm find-ltrm-eui eui)
-(def-lazy-reader lexterm s#typ find-ltyp-eui eui)
-
-;; LEX SQL Read functions
-
-(defun find-labr-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,ABR,EUI2,BAS2 from LRABR where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'labr :eui eui
- :bas (nth 0 tuple)
- :abr (nth 1 tuple)
- :eui2 (ensure-integer (nth 2 tuple))
- :bas2 (nth 3 tuple))
- results))
- (nreverse results))))
-
-(defun find-labr-bas (bas)
- (gu:awhen (mutex-sql-query
- (format nil "select EUI,ABR,EUI2,BAS2 from LRABR where BAS='~a'" bas))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'labr :eui (ensure-integer (nth 0 tuple))
- :bas (copy-seq bas)
- :abr (nth 1 tuple)
- :eui2 (ensure-integer (nth 2 tuple))
- :bas2 (nth 3 tuple))
- results))
- (nreverse results))))
-
-(defun find-lagr-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select STR,SCA,AGR,CIT,BAS from LRAGR where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lagr
- :eui eui
- :str (nth 0 tuple)
- :sca (nth 1 tuple)
- :agr (nth 2 tuple)
- :cit (nth 3 tuple)
- :bas (nth 4 tuple))
- results))
- (nreverse results))))
-
-(defun find-lcmp-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,SCA,COM from LRCMP where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lcmp
- :eui eui
- :bas (nth 0 tuple)
- :sca (nth 1 tuple)
- :com (nth 2 tuple))
- results))
- (nreverse results))))
-
-(defun find-lmod-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,SCA,PSN_MOD,FEA from LRMOD where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lmod
- :eui eui
- :bas (nth 0 tuple)
- :sca (nth 1 tuple)
- :psnmod (nth 2 tuple)
- :fea (nth 3 tuple))
- results))
- (nreverse results))))
-
-(defun find-lnom-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,SCA,EUI2,BAS2,SCA2 from LRNOM where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lnom
- :eui eui
- :bas (nth 0 tuple)
- :sca (nth 1 tuple)
- :eui2 (ensure-integer (nth 2 tuple))
- :bas2 (nth 3 tuple)
- :sca2 (nth 4 tuple))
- results))
- (nreverse results))))
-
-(defun find-lprn-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,NUM,GND,CAS,POS,QNT,FEA from LRPRN where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lprn
- :eui eui
- :bas (nth 0 tuple)
- :num (nth 1 tuple)
- :gnd (nth 2 tuple)
- :cas (nth 3 tuple)
- :pos (nth 4 tuple)
- :qnt (nth 5 tuple)
- :fea (nth 6 tuple))
- results))
- (nreverse results))))
-
-(defun find-lprp-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,STR,SCA,FEA from LRPRP where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lprp
- :eui eui
- :bas (nth 0 tuple)
- :str (nth 1 tuple)
- :sca (nth 2 tuple)
- :fea (nth 3 tuple))
- results))
- (nreverse results))))
-
-(defun find-lspl-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select SPV,BAS from LRSPL where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'lspl
- :eui eui
- :spv (nth 0 tuple)
- :bas (nth 1 tuple))
- results))
- (nreverse results))))
-
-
-(defun find-ltrm-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,GEN from LRTRM where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'ltrm
- :eui eui
- :bas (nth 0 tuple)
- :gen (nth 1 tuple))
- results))
- (nreverse results))))
-
-(defun find-ltyp-eui (eui)
- (gu:awhen (mutex-sql-query
- (format nil "select BAS,SCA,TYP from LRTYP where EUI=~d" eui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'ltyp
- :eui eui
- :bas (nth 0 tuple)
- :sca (nth 1 tuple)
- :typ (nth 2 tuple))
- results))
- (nreverse results))))
-
-(defun find-lwd-wrd (wrd)
- (gu:awhen (mutex-sql-query
- (format nil "select EUI from LRWD where WRD='~a'" wrd))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push (ensure-integer (nth 0 tuple)) results))
- (make-instance 'lwd :wrd wrd
- :euilist (nreverse results)))))
-
-;;; Semantic Network SQL access functions
-
-(defun find-sdef-ui (ui)
- (gu:awhen (car (mutex-sql-query
- (format nil "select RT,STY_RL,STN_RTN,DEF,EX,UN,RH,ABR,RIN from SRDEF where UI=~d" ui)))
- (make-instance 'sdef :rt (nth 0 gu::it)
- :ui ui
- :styrl (nth 1 gu::it)
- :stnrtn (nth 2 gu::it)
- :def (nth 3 gu::it)
- :ex (nth 4 gu::it)
- :un (nth 5 gu::it)
- :rh (nth 6 gu::it)
- :abr (nth 7 gu::it)
- :rin (nth 8 gu::it))))
-
-(defun find-sstre1-ui (ui)
- (gu:awhen (mutex-sql-query
- (format nil "select UI2,UI3 from SRSTRE1 where UI=~d" ui))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'sstre1 :ui ui
- :ui2 (ensure-integer (nth 0 tuple))
- :ui3 (ensure-integer (nth 1 tuple)))
- results))
- (nreverse results))))
-
-(defun find-sstre1-ui2 (ui2)
- (gu:awhen (mutex-sql-query
- (format nil "select UI,UI3 from SRSTRE1 where UI2=~d" ui2))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'sstre1 :ui (ensure-integer (nth 0 tuple))
- :ui2 ui2
- :ui3 (ensure-integer (nth 1 tuple)))
- results))
- (nreverse results))))
-
-(defun find-sstr-rl (rl)
- (gu:awhen (mutex-sql-query
- (format nil "select STY_RL,STY_RL2,LS from SRSTRE where RL='~a'" rl))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'sstr
- :rl rl
- :styrl (nth 0 tuple)
- :styrl2 (nth 1 tuple)
- :ls (nth 2 tuple))
- results))
- (nreverse results))))
-
-
-(defun find-sstre2-sty (sty)
- (gu:awhen (mutex-sql-query
- (format nil "select RL,STY2 from SRSTRE2 where STY='~a'" sty))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'sstre2
- :sty (copy-seq sty)
- :rl (nth 0 tuple)
- :sty2 (nth 1 tuple))
- results))
- (nreverse results))))
-
-(defun find-sstr-styrl (styrl)
- (gu:awhen (mutex-sql-query
- (format nil "select RL,STY_RL2,LS from SRSTR where RL='~a'" styrl))
- (let ((results '()))
- (dolist (tuple gu::it)
- (push
- (make-instance 'sstr :styrl styrl
- :rl (nth 0 tuple)
- :styrl2 (nth 1 tuple)
- :ls (nth 2 tuple))
- results))
- (nreverse results))))
-
-
+++ /dev/null
-;;; $Id: obj.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
-;;;
-;;; UMLS object defintions and printing routines
-
-(in-package :umlisp)
-(declaim (optimize (speed 3) (safety 1)))
-
-(defclass umlsclass ()
- ()
- (:metaclass ml-class)
- (:documentation "Parent class of all UMLS objects"))
-
-
-(defmethod print-object ((obj umlsclass) (s stream))
- (print-unreadable-object (obj s :type t :identity t)
- (let ((fmt (make-instance 'gu.ml::textformat)))
- (apply #'format
- s (funcall (gu.ml::obj-data-fmtstr fmt) obj)
- (multiple-value-list
- (funcall (funcall (gu.ml::obj-data-value-func fmt) obj) obj))))))
-
-
-(defclass umlisp-user (umlsclass)
- ((id :type fixnum :initarg :id :reader id)
- (first-name :type string :initarg :first-name :reader first-name)
- (last-name :type string :initarg :last-name :reader last-name)
- (organization :type string :initarg :organization :reader organization)
- (address1 :type string :initarg :address1 :reader address1)
- (address2 :type string :initarg :address2 :reader address2)
- (city :type string :initarg :city :reader city)
- (state :type string :initarg :state :reader state)
- (zip :type string :initarg :zip :reader zip)
- (country :type string :initarg :country :reader country)
- (licensed :type boolean :initarg :licensed :reader licensed)
- (occupation :type string :initarg :occupation :reader occupation)
- (email :type string :initarg :email :reader email)
- (passwd :type string :initarg :passwd :reader passwd)
- (srl :type fixnum :initarg :srl :reader srl)
- (timeout :type fixnum :initarg :timeout :reader timeout)
- (maillist :type boolean :initarg :maillist :reader maillist)
- (datetime-created :type string :initarg :datetime-created
- :reader datetime-created)
- (datetime-modified :type string :initarg :datetime-modified
- :reader datetime-modified))
- (:default-initargs
- :id nil :first-name nil :last-name nil :email nil :passwd nil :srl nil
- :organization nil :address1 nil :address2 nil :city nil :state nil
- :zip nil :country nil :licensed nil :occupation nil :maillist nil
- :timeout nil :datetime-created nil :datetime-modified nil)
- (:metaclass ml-class)
- (:title "UMLisp User")
- (:fields
- (id :fixnum) (first-name :string) (last-name :string) (email :string)
- (occupation :string) (organization :string) (address1 :string)
- (address2 :string) (city :string) (state :string) (zip :string)
- (country :string) (licensed :boolean) (maillist :boolean) (srl :fixnum)
- (timeout :fixnum) (datetime-created :string) (datetime-modified :string))
- (:documentation "Class for UMLisp user database"))
-
-(defclass ustats (umlsclass)
- ((name :type string :initarg :name :reader name)
- (hits :type integer :initarg :hits :reader hits)
- (srl :type fixnum :initarg :srl :reader srl))
- (:metaclass ml-class)
- (:default-initargs :name nil :hits nil :srl nil)
- (:title "UMLS Statistic")
- (:fields (name :string) (hits :commainteger) (srl :fixnum))
- (:documentation "Custom Table: UMLS Database statistics."))
-
-(defclass usrl (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (srl :type integer :initarg :srl :reader srl))
- (:metaclass ml-class)
- (:default-initargs :sab nil :srl nil)
- (:title "Source Restriction Level")
- (:fields (sab :string) (srl :fixnum))
- (:documentation "Custom Table: Source Restriction Level"))
-
-(defclass bsab (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (name :type string :initarg :name :reader name)
- (hits :type fixnum :initarg :hits :reader hits))
- (:metaclass ml-class)
- (:default-initargs :sab nil :name nil :hits nil)
- (:title "Source of Abbreviation")
- (:fields (sab :string) (name :string) (hits :commainteger))
- (:ref-fields (sab find-ustr-sab (("subobjects" "no"))))
- (:documentation "Bonus SAB file"))
-
-(defclass btty (umlsclass)
- ((tty :type string :initarg :tty :reader tty)
- (name :type string :initarg :name :reader name))
- (:metaclass ml-class)
- (:default-initargs :tty nil :name nil)
- (:title "Bonus TTY")
- (:fields (tty :string) (name :fixnum))
- (:documentation "Bonus TTY file"))
-
-(defclass brel (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (sl :type string :initarg :sl :reader sl)
- (rel :type string :initarg :rel :reader rel)
- (rela :type string :initarg :rela :reader rela)
- (hits :type fixnum :initarg :hits :reader hits))
- (:metaclass ml-class)
- (:default-initargs :sab nil :sl nil :rel nil :rela nil :hits nil)
- (:title "Bonus REL")
- (:fields
- (sab :string) (sl :string) (rel :string) (rela :string) (hits :commainteger))
- (:documentation "Bonus REL file"))
-
-(defclass batn (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (atn :type string :initarg :atn :reader atn)
- (hits :type fixnum :initarg :hits :reader hits))
- (:metaclass ml-class)
- (:default-initargs :sab nil :atn nil)
- (:title "Bonus ATN")
- (:fields (sab :string) (atn :string) (hits :commaninteger))
- (:documentation "Bonus ATN file"))
-
-(defclass urank (umlsclass)
- ((rank :type fixnum :initarg :rank :reader rank)
- (sab :type string :initarg :sab :reader sab)
- (tty :type string :initarg :tty :reader tty)
- (supres :type string :initarg :supres :reader supres))
- (:metaclass ml-class)
- (:default-initargs :rank nil :sab nil :tty nil :supres nil)
- (:title "Rank")
- (:fields (rank :fixnum) (sab :string) (tty :string) (supres :string)))
-
-(defclass udef (umlsclass)
- ((def :type string :initarg :def :reader def)
- (sab :type string :initarg :sab :reader sab))
- (:metaclass ml-class)
- (:default-initargs :def nil :sab nil)
- (:title "Definition")
- (:ref-fields (sab find-bsab-sab))
- (:fields (sab :string) (def :cdata)))
-
-(defclass usat (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (code :type string :initarg :code :reader code)
- (atn :type string :initarg :atn :reader atn)
- (atv :type string :initarg :atv :reader atv))
- (:metaclass ml-class)
- (:default-initargs :sab nil :code nil :atn nil :atv nil)
- (:title "Simple Attribute")
- (:ref-fields (sab find-bsab-sab))
- (:fields (sab :string) (code :string) (atn :string) (atv :cdata)))
-
-(defclass uso (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (code :type string :initarg :code :reader code)
- (tty :type string :initarg :tty :reader tty)
- (srl :type fixnum :initarg :srl :reader srl))
- (:metaclass ml-class)
- (:default-initargs :sab nil :code nil :tty nil :srl nil)
- (:title "Source")
- (:ref-fields (sab find-bsab-sab) (tty find-btty-tty))
- (:fields (sab :string) (code :string) (tty :string) (srl :fixnum)))
-
-(defclass ucxt (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (code :type string :initarg :code :reader code)
- (rnk :type fixnum :initarg :rnk :reader rnk)
- (cxn :type fixnum :initarg :cxn :reader cxn)
- (cxl :type string :initarg :cxl :reader cxl)
- (cxs :type string :initarg :cxs :reader cxs)
- (cui2 :type fixnum :initarg :cui2 :reader cui2)
- (hcd :type string :initarg :hcd :reader hcd)
- (rela :type string :initarg :rela :reader rela)
- (xc :type string :initarg :xc :reader xc))
- (:metaclass ml-class)
- (:default-initargs :sab nil :code nil :rnk nil :cxn nil :cxl nil :cxs nil
- :cui2 nil :hcd nil :rela nil :xc nil)
- (:title "Context")
- (:ref-fields (sab find-bsab-sab) (cui2 find-ucon-cui))
- (:fields
- (sab :string) (code :string) (rnk :fixnum) (cxn :fixnum) (cxl :string)
- (hcd :string) (rela :string) (xc :string) (cui2 :string fmt-cui)
- (cxs :cdata)))
-
-(defclass ustr (umlsclass)
- ((sui :type fixnum :initarg :sui :reader sui)
- (cui :type fixnum :initarg :cui :reader cui)
- (lui :type fixnum :initarg :lui :reader lui)
- (cuisui :type integer :initarg :cuisui :reader cuisui )
- (str :type string :initarg :str :reader str)
- (lrl :type fixnum :initarg :lrl :reader lrl)
- (stt :type string :initarg :stt :reader stt)
- (s#sat :reader s#sat)
- (s#so :reader s#so)
- (s#cxt :reader s#cxt))
- (:metaclass ml-class)
- (:default-initargs
- :sui nil :cui nil :lui nil :cuisui nil :str nil :lrl nil :stt nil)
- (:title "String")
- (:subobjects-lists (s#sat usat) (s#so uso) (s#cxt ucxt))
- (:fields (sui :string fmt-sui) (stt :string) (lrl :fixnum) (str :cdata))
- (:ref-fields (sui find-ustr-sui)))
-
-(defclass ulo (umlsclass)
- ((isn :type string :initarg :isn :reader isn)
- (fr :type fixnum :initarg :fr :reader fr)
- (un :type string :initarg :un :reader un)
- (sui :type fixnum :initarg :sui :reader sui)
- (sna :type string :initarg :sna :reader sna)
- (soui :type string :initarg :soui :reader soui))
- (:metaclass ml-class)
- (:default-initargs :isn nil :fr nil :un nil :sui nil :sna nil :soui nil)
- (:title "Locator")
- (:fields (isn :string) (fr :fixnum) (un :string) (sna :string)
- (soui :string) (sui :string fmt-sui) (suistr :string)))
-
-(defclass uterm (umlsclass)
- ((lui :type fixnum :initarg :lui :reader lui)
- (cui :type fixnum :initarg :cui :reader cui)
- (lat :type string :initarg :lat :reader lat)
- (ts :type string :initarg :ts :reader ts)
- (lrl :type fixnum :initarg :lrl :reader lrl)
- (s#str :reader s#str)
- (s#sat :reader s#sat))
- (:metaclass ml-class)
- (:default-initargs :lui nil :cui nil :lat nil :ts nil :lrl nil)
- (:title "Term")
- (:subobjects-lists (s#sat usat) (s#str ustr))
- (:fields (lui :string fmt-lui) (lat :string) (ts :string) (lrl :fixnum))
- (:ref-fields (lui find-uterm-lui)))
-
-(defclass usty (umlsclass)
- ((tui :type fixnum :initarg :tui :reader tui)
- (sty :type string :initarg :sty :reader sty))
- (:metaclass ml-class)
- (:default-initargs :tui nil :sty nil)
- (:title "Semantic Type")
- (:ref-fields (tui find-ucon-tui (("subobjects" "no"))))
- (:fields (tui :string fmt-tui) (sty :string)))
-
-(defclass urel (umlsclass)
- ((rel :type string :initarg :rel :reader rel)
- (cui1 :type fixnum :initarg :cui1 :reader cui1)
- (cui2 :type fixnum :initarg :cui2 :reader cui2)
- (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
- (rela :type string :initarg :rela :reader rela)
- (sab :type string :initarg :sab :reader sab)
- (sl :type string :initarg :sl :reader sl)
- (mg :type string :initarg :mg :reader mg))
- (:metaclass ml-class)
- (:default-initargs
- :rel nil :cui1 nil :cui2 nil :pfstr2 nil :rela nil :sab nil :sl nil :mg nil)
- (:title "Relationship")
- (:ref-fields (rel find-brel-rel) (sab find-bsab-sab) (cui2 find-ucon-cui))
- (:fields (rel :string) (rela :string) (sab :string) (sl :string)
- (mg :string) (cui2 :string fmt-cui) (pfstr2 :cdata)))
-
-(defclass ucoc (umlsclass)
- ((cui1 :type fixnum :initarg :cui1 :reader cui1)
- (cui2 :type fixnum :initarg :cui2 :reader cui2)
- (pfstr2 :type string :initarg :pfstr2 :reader pfstr2)
- (soc :type string :initarg :soc :reader soc)
- (cot :type string :initarg :cot :reader cot)
- (cof :type fixnum :initarg :cof :reader cof)
- (coa :type string :initarg :coa :reader coa))
- (:metaclass ml-class)
- (:default-initargs
- :cui1 nil :cui2 nil :pfstr2 nil :soc nil :cot nil :cof nil :coa nil)
- (:title "Co-occuring Concept")
- (:ref-fields (cui2 find-ucon-cui))
- (:fields (soc :string) (cot :string) (cof :fixnum) (coa :cdata)
- (cui2 :string fmt-cui) (pfstr2 :cdata)))
-
-
-(defclass uatx (umlsclass)
- ((sab :type string :initarg :sab :reader sab)
- (rel :type string :initarg :rel :reader rel)
- (atx :type string :initarg :atx :reader atx))
- (:metaclass ml-class)
- (:default-initargs :sab nil :rel nil :atx nil)
- (:title "Associated Expression")
- (:fields (sab :string) (rel :string) (atx :cdata)))
-
-(defclass ucon (umlsclass)
- ((cui :type fixnum :initarg :cui :reader cui )
- (pfstr :initarg :pfstr :reader pfstr)
- (lrl :initarg :lrl :reader lrl)
- (s#term :reader s#term)
- (s#def :reader s#def)
- (s#lo :reader s#lo)
- (s#rel :reader s#rel)
- (s#coc :reader s#coc)
- (s#sat :reader s#sat)
- (s#atx :reader s#atx)
- (s#sty :reader s#sty))
- (:metaclass ml-class)
- (:default-initargs :cui nil :pfstr nil :lrl nil)
- (:title "Concept")
- (:subobjects-lists
- (s#def udef) (s#sty usty) (s#lo ulo) (s#atx uatx) (s#sat usat) (s#rel urel)
- (s#coc ucoc) (s#term uterm))
- (:fields (cui :string fmt-cui) (lrl :fixum) (pfstr :cdata))
- (:ref-fields (cui find-ucon-cui)))
-
-(defclass uxw (umlsclass)
- ((wd :type string :initarg :wd :reader wd)
- (cui :type fixnum :initform nil :initarg :cui :reader cui)
- (lui :type fixnum :initform nil :initarg :lui :reader lui)
- (sui :type fixnum :initform nil :initarg :sui :reader sui))
- (:metaclass ml-class)
- (:default-initargs :wd nil :cui nil :lui nil :sui nil)
- (:title "XW Index")
- (:fields (wd :string) (cui :string fmt-cui) (lui :string fmt-lui)
- (sui :string fmt-sui)))
-
-(defclass uxnw (umlsclass)
- ((lat :type string :initarg :lat :reader lat)
- (nwd :type string :initarg :nwd :reader nwd)
- (cuilist :type list :initarg :cuilist :reader uxnw-cuilist))
- (:metaclass ml-class)
- (:default-initargs :lat nil :nwd nil :cuilist nil)
- (:title "XNW Index")
- (:fields (lat :string) (nwd :string) (cuilist :string)))
-
-(defclass uxns (umlsclass)
- ((lat :type string :initarg :lat :reader lat)
- (nstr :type string :initarg :nstr :reader nstr)
- (cuilist :type list :initarg :cuilist :reader cuilist))
- (:metaclass ml-class)
- (:default-initargs :lat nil :nstr nil :cuilist nil)
- (:title "XNS Index")
- (:fields (lat :string) (nstr :string) (cuilist :string)))
-
-
-;;; LEX objects
-
-(defclass lexterm (umlsclass)
- ((eui :type fixnum :initarg :eui :reader eui)
- (wrd :type string :initarg :wrd :reader wrd)
- (s#abr :reader s#abr)
- (s#agr :reader s#agr)
- (s#cmp :reader s#cmp)
- (s#mod :reader s#mod)
- (s#nom :reader s#nom)
- (s#prn :reader s#prn)
- (s#prp :reader s#prp)
- (s#spl :reader s#spl)
- (s#trm :reader s#trm)
- (s#typ :reader s#typ))
- (:metaclass ml-class)
- (:default-initargs :eui nil :wrd nil)
- (:title "Lexical Term")
- (:subobjects-lists
- (s#abr labr) (s#agr lagr) (s#cmp lcmp) (s#mod lmod) (s#nom unom)
- (s#prn lprn) (s#prp lprp) (s#spl lspl) (s#trm ltrm) (s#typ ltyp))
- (:fields (eui :string fmt-eui) (wrd :string))
- (:ref-fields (eui find-lexterm-eui)))
-
-
-(defclass labr (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (abr :type string :initarg :abr :reader abr)
- (eui2 :type integer :initarg :eui2 :reader eui2)
- (bas2 :type string :initarg :bas2 :reader bas2))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :abr nil :eui2 nil :bas2 nil)
- (:title "Abbreviations and Acronyms")
- (:fields (eui :string fmt-eui) (bas :string) (abr :string)
- (eui2 :string fmt-eui) (bas2 :string )))
-
-(defclass lagr (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (str :type string :initarg :str :reader str)
- (sca :type string :initarg :sca :reader sca)
- (agr :type string :initarg :agr :reader agr)
- (cit :type string :initarg :cit :reader cit)
- (bas :type string :initarg :bas :reader bas))
- (:metaclass ml-class)
- (:default-initargs :eui nil :str nil :sca nil :agr nil :cit nil :bas nil)
- (:title "Agreement and Inflection")
- (:fields (eui :string fmt-eui) (str :string) (sca :string) (agr :string)
- (cit :string) (bas :string)))
-
-(defclass lcmp (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (sca :type string :initarg :sca :reader sca)
- (com :type string :initarg :com :reader com))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :sca nil :com nil)
- (:title "Complementation")
- (:fields (eui :string fmt-eui) (bas :string) (sca :string) (com :string)))
-
-(defclass lmod (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (sca :type string :initarg :sca :reader sca)
- (psnmod :type string :initarg :psnmod :reader psnmod)
- (fea :type string :initarg :fea :reader fea))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :sca nil :psnmod nil :fea nil)
- (:title "Modifiers")
- (:fields (eui :string fmt-eui) (bas :string) (sca :string) (psnmod :string)
- (fea :string)))
-
-(defclass lnom (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (sca :type string :initarg :sca :reader sca)
- (eui2 :type integer :initarg :eui2 :reader eui2)
- (bas2 :type string :initarg :bas2 :reader bas2)
- (sca2 :type string :initarg :sca2 :reader sca2))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :sca nil :eui2 nil :bas2 nil :sca2 nil)
- (:title "Nominalizations")
- (:fields (eui :string fmt-eui) (bas :string) (sca :string)
- (eui2 :string fmt-eui) (bas2 :string) (sca2 :string)))
-
-(defclass lprn (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (num :type string :initarg :num :reader num)
- (gnd :type string :initarg :gnd :reader gnd)
- (cas :type string :initarg :cas :reader cas)
- (pos :type string :initarg :pos :reader pos)
- (qnt :type string :initarg :qnt :reader qnt)
- (fea :type string :initarg :fea :reader fea))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :num nil :gnd nil :cas nil
- :pos nil :qnt nil :fea nil)
- (:title "Pronouns")
- (:fields (eui :string fmt-eui) (bas :string) (num :string) (gnd :string)
- (cas :string) (pos :string) (qnt :string) (fea :string)))
-
-(defclass lprp (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (str :type string :initarg :str :reader str)
- (sca :type string :initarg :sca :reader sca)
- (fea :type string :initarg :fea :reader fea))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :str nil :sca nil :fea nil)
- (:title "Properties")
- (:fields (eui :string fmt-eui) (bas :string) (str :string) (sca :string)
- (fea :string)))
-
-
-(defclass lspl (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (spv :type string :initarg :spv :reader spv)
- (bas :type string :initarg :bas :reader bas))
- (:metaclass ml-class)
- (:default-initargs :eui nil :spv nil :bas nil)
- (:title "Spelling Variants")
- (:fields (eui :string fmt-eui) (spv :string) (bas :string)))
-
-
-
-(defclass ltrm (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (gen :type string :initarg :gen :reader gen))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :gen nil)
- (:title "Trade Marks")
- (:fields (eui :string fmt-eui) (bas :string) (gen :string)))
-
-(defclass ltyp (umlsclass)
- ((eui :type integer :initarg :eui :reader eui)
- (bas :type string :initarg :bas :reader bas)
- (sca :type string :initarg :sca :reader sca)
- (typ :type string :initarg :typ :reader typ))
- (:metaclass ml-class)
- (:default-initargs :eui nil :bas nil :sca nil :typ nil)
- (:title "Inflection Type")
- (:fields (eui :string fmt-eui) (bas :string) (sca :string) (typ :string)))
-
-(defclass lwd (umlsclass)
- ((wrd :type string :initarg :wrd :reader wrd)
- (euilist :type list :initarg :euilist :reader euilist))
- (:metaclass ml-class)
- (:default-initargs :wrd nil :euilist nil)
- (:title "Lexical Word Index")
- (:fields (wrd :string) (euilist :string)))
-
-;;; Semantic NET objects
-
-(defclass sdef (umlsclass)
- ((rt :type string :initarg :rt :reader rt)
- (ui :type integer :initarg :ui :reader ui)
- (styrl :type string :initarg :styrl :reader styrl)
- (stnrtn :type string :initarg :stnrtn :reader stnrtn)
- (def :type string :initarg :def :reader def)
- (ex :type string :initarg :ex :reader ex)
- (un :type string :initarg :un :reader un)
- (rh :type string :initarg :rh :reader rh)
- (abr :type string :initarg :abr :reader abr)
- (rin :type string :initarg :rin :reader rin))
- (:metaclass ml-class)
- (:default-initargs
- :rt nil :ui nil :styrl nil :stnrtn nil :def nil :ex nil :un nil :rh nil
- :abr nil :rin nil)
- (:title "Basic information about Semantic Types and Relations")
- (:fields
- (rt :string) (ui :string fmt-tui) (styrl :string) (stnrtn :string-tui)
- (def :string) (ex :string) (un :string) (rh :string) (abr :string)
- (rin :string)))
-
-(defclass sstr (umlsclass)
- ((styrl :type string :initarg :styrl :reader styrl)
- (rl :type string :initarg :rl :reader rl)
- (styrl2 :type string :initarg :styrl2 :reader styrl2)
- (ls :type string :initarg :ls :reader ls))
- (:metaclass ml-class)
- (:default-initargs :styrl nil :rl nil :styrl2 nil :ls nil)
- (:title "Structure of the Network")
- (:fields (styrl :string) (rl :string) (styrl2 :string) (ls :string)))
-
-(defclass sstre1 (umlsclass)
- ((ui :type integer :initarg :ui :reader ui)
- (ui2 :type integer :initarg :ui2 :reader ui2)
- (ui3 :type integer :initarg :ui3 :reader ui3))
- (:metaclass ml-class)
- (:default-initargs :ui nil :ui2 nil :ui3 nil)
- (:title "Fully Inherited Set of Releatons (TUI's)")
- (:fields (ui :string fmt-tui) (ui2 :string fmt-tui) (ui3 :string fmt-tui)))
-
-(defclass sstre2 (umlsclass)
- ((sty :type string :initarg :ui :reader sty)
- (rl :type string :initarg :ui2 :reader rl)
- (sty2 :type string :initarg :ui3 :reader sty2))
- (:metaclass ml-class)
- (:default-initargs :sty nil :rl nil :sty2 nil)
- (:title "Fully Inherited Set of Releatons (strings)")
- (:fields (sty :string) (rl :string) (sty2 :string)))
-
-;;; Formatting routines
-
-(defmethod fmt-cui ((c ucon))
- (format nil "C~7,'0d" (cui c)))
-
-(defmethod fmt-cui ((c fixnum))
- (format nil "C~7,'0d" c))
-
-(defmethod fmt-cui ((c string))
- (if (eql (aref c 0) #\C)
- c
- (format nil "C~7,'0d" (parse-integer c))))
-
-(defmethod fmt-cui ((c null))
- (format nil "nil"))
-
-(defmethod fmt-lui ((l uterm))
- (format nil "L~7,'0d" (lui l)))
-
-(defmethod fmt-lui ((l fixnum))
- (format nil "L~7,'0d" l))
-
-(defmethod fmt-lui ((l string))
- (if (eql (aref l 0) #\L)
- l
- (format nil "L~7,'0d" (parse-integer l))))
-
-(defmethod fmt-sui ((s ustr))
- (format nil "S~7,'0d" (sui s)))
-
-(defmethod fmt-sui ((s fixnum))
- (format nil "S~7,'0d" s))
-
-(defmethod fmt-sui ((s string))
- (if (eql (aref s 0) #\S)
- s
- (format nil "S~7,'0d" (parse-integer s))))
-
-(defmethod fmt-tui ((s fixnum))
- (format nil "T~3,'0d" s))
-
-(defmethod fmt-tui ((s string))
- (if (eql (aref s 0) #\T)
- s
- (format nil "T~3,'0d" (parse-integer s))))
-
-(defmethod fmt-eui ((e fixnum))
- (format nil "E~7,'0d" e))
-
-(defmethod fmt-eui ((e string))
- (if (eql (aref e 0) #\E)
- e
- (format nil "E~7,'0d" (parse-integer e))))
-
-(defmethod fmt-eui ((e null))
- (format nil "nil"))
-
-;;; Generic display functions
-
-(eval-when (:compile-toplevel :load-toplevel :execute)
-(defun english-term-p (obj)
- (and (eq (class-name (class-of obj)) 'uterm)
- (string-equal (lat obj) "ENG"))))
-
-(defun display-umls-obj
- (obj &key (os *standard-output*) (format :text) (label nil)
- (file-wrapper t) (english-only nil) (subobjects nil)
- (refvars nil))
- (display-ml-class
- obj :os os :format format :label label :subobjects subobjects
- :file-wrapper file-wrapper
- :english-only-function (if english-only #'english-term-p nil)
- :refvars refvars))
-
-(defmacro defludisp-ml-class (newfuncname lookup-func)
- "Defines functions for looking up and displaying objects"
- `(defun ,newfuncname
- (keyval &key (os *standard-output*) (format :text) (label nil)
- (file-wrapper t) (english-only nil) (subobjects nil))
- (let ((obj (funcall ,lookup-func keyval)))
- (display-umls-obj obj :os os :format format :label label
- :file-wrapper file-wrapper :english-only english-only
- :subobjects subobjects))))
-
-(defludisp-ml-class disp-con #'find-ucon-cui)
-(defludisp-ml-class disp-term #'find-uterm-lui)
-(defludisp-ml-class disp-str #'find-ustr-sui)
-
--- /dev/null
+;;; $Id: sql-classes.lisp,v 1.1 2002/10/08 22:08:56 kevin Exp $
+
+(in-package :umlisp)
+
+(declaim (optimize (speed 3) (safety 1)))
+
+(defvar *current-srl* nil)
+(defun current-srl ()
+ *current-srl*)
+(defun current-srl! (srl)
+ (setq *current-srl* srl))
+
+
+;;; Accessors (read on demand)
+
+;; defines a slot-unbound method for class and slot-name, fills
+;; the slot by calling reader function with the slot values of
+;; the instance's reader-keys
+(defmacro def-lazy-reader (class slot-name reader &rest reader-keys)
+ (let* ((the-slot-name (gensym))
+ (the-class (gensym))
+ (the-instance (gensym))
+ (keys '()))
+ (dolist (key reader-keys)
+ (push (list 'slot-value the-instance (list 'quote key)) keys))
+ (setq keys (nreverse keys))
+ `(defmethod slot-unbound (,the-class (,the-instance ,class)
+ (,the-slot-name (eql ',slot-name)))
+ (declare (ignore ,the-class))
+ (setf (slot-value ,the-instance ,the-slot-name)
+ (,reader ,@keys)))))
+
+(def-lazy-reader ucon s#term find-uterm-cui cui)
+(def-lazy-reader ucon s#def find-udef-cui cui)
+(def-lazy-reader ucon s#sty find-usty-cui cui)
+(def-lazy-reader ucon s#rel find-urel-cui cui)
+(def-lazy-reader ucon s#coc find-ucoc-cui cui)
+(def-lazy-reader ucon s#lo find-ulo-cui cui)
+(def-lazy-reader ucon s#atx find-uatx-cui cui)
+(def-lazy-reader ucon s#sat find-usat-ui cui)
+
+;; For uterms
+(def-lazy-reader uterm s#str find-ustr-cuilui cui lui)
+(def-lazy-reader uterm s#sat find-usat-ui cui lui)
+
+;; For ustrs
+(def-lazy-reader ustr s#sat find-usat-ui cui lui sui)
+(def-lazy-reader ustr s#cxt find-ucxt-cuisui cui sui)
+(def-lazy-reader ustr s#so find-uso-cuisui cui sui)
+
+;;; Object lookups
+
+;;; Lookup functions for uterms,ustr in ucons
+
+(defun find-uterm-in-ucon (ucon lui)
+ (find lui (s#term ucon) :key #'uterm-lui :test 'equal))
+
+(defun find-ustr-in-uterm (uterm sui)
+ (find sui (s#str uterm) :key #'ustr-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))
+
+
+(defun find-ucon-cui (cui &key (srl *current-srl*))
+ "Find ucon for a cui"
+ (if (stringp cui)
+ (setq cui (parse-cui cui)))
+ (if cui
+ (let ((ls (format nil "select KPFSTR,KCUILRL from MRCON where CUI=~d"
+ cui)))
+ (if srl
+ (string-append ls (format nil " and KCUILRL <= ~d limit 1" srl))
+ (string-append ls " limit 1"))
+ (gu:awhen (car (mutex-sql-query ls))
+ (make-instance 'ucon :cui cui :pfstr (car gu::it)
+ :lrl (ensure-integer (cadr gu::it)))))
+ nil))
+
+(defun find-ucon-lui (lui &key (srl *current-srl*))
+ "Find list of ucon for lui"
+ (if (stringp lui)
+ (setq lui (parse-lui lui)))
+ (if lui
+ (let ((ucons '())
+ (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where LUI=~d" lui)))
+ (if srl
+ (string-append ls (format nil " and KCUILRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
+ :pfstr (nth 1 tuple)
+ :lrl (ensure-integer (nth 2 tuple)))
+ ucons))
+ (nreverse ucons))
+ nil))
+
+(defun find-ucon-sui (sui &key (srl *current-srl*))
+ "Find list of ucon for sui"
+ (if (stringp sui)
+ (setq sui (parse-sui sui)))
+ (if sui
+ (let ((ucons '())
+ (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where SUI=~d" sui)))
+ (when srl
+ (string-append ls (format nil " and KCUILRL <= ~d" srl)))
+ (let ((tuples (mutex-sql-query ls)))
+ (dolist (tuple tuples)
+ (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
+ :pfstr (nth 1 tuple)
+ :lrl (ensure-integer (nth 2 tuple)))
+ ucons)))
+ (nreverse ucons))
+ nil))
+
+(defun find-ucon-cuisui (cui sui &key (srl *current-srl*))
+ "Find ucon for cui/sui"
+ (if (stringp cui)
+ (setq cui (parse-cui cui)))
+ (if (stringp sui)
+ (setq sui (parse-sui sui)))
+ (if (and cui sui)
+ (let ((ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where KCUISUI=~d"
+ (make-cuisui cui sui))))
+ (when srl
+ (string-append ls (format nil " and KCUILRL <= ~d" srl)))
+ (gu:aif (car (mutex-sql-query ls))
+ (make-instance 'ucon :cui (ensure-integer (nth 0 gu::it))
+ :pfstr (nth 1 gu::it)
+ :lrl (ensure-integer (nth 2 gu::it)))
+ nil))
+ nil))
+
+(defun find-ucon-str (str &key (srl *current-srl*))
+ "Find ucon that are exact match for str"
+ (if str
+ (let ((ucons '())
+ (ls (format nil "select distinct CUI,KPFSTR,KCUILRL from MRCON where STR='~a'" str)))
+ (when srl
+ (string-append ls " and KCUILRL <= ~d" srl))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'ucon :cui (ensure-integer (nth 0 tuple))
+ :pfstr (nth 1 tuple)
+ :lrl (ensure-integer (nth 2 tuple))) ucons))
+ (nreverse ucons))
+ nil))
+
+(defun find-ucon-all (&key (srl *current-srl*))
+ "Return list of all ucon's"
+ (let ((ls "select distinct CUI,KPFSTR,KCUILRL from MRCON"))
+ (when srl
+ (string-append ls (format nil " where KCUILRL <= ~d" srl)))
+ (string-append ls " order by CUI asc")
+ (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)))
+ ls
+ :database db))))
+
+
+
+(defun find-udef-cui (cui &key (srl *current-srl*))
+ "Return a list of udefs for cui"
+ (let ((udefs '())
+ (ls (format nil "select SAB,DEF from MRDEF where CUI=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'udef :sab (car tuple) :def (cadr tuple)) udefs))
+ (nreverse udefs)))
+
+(defun find-usty-cui (cui &key (srl *current-srl*))
+ "Return a list of usty for cui"
+ (let ((ustys '())
+ (ls (format nil "select TUI,STY from MRSTY where CUI=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
+ ustys))
+
+(defun find-usty-word (word &key (srl *current-srl*))
+ "Return a list of usty that match word"
+ (let ((ustys '())
+ (ls (format nil "select distinct TUI,STY from MRSTY where STY like '%~a%'" word)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'usty :tui (ensure-integer (car tuple)) :sty (cadr tuple)) ustys))
+ ustys))
+
+(defun find-urel-cui (cui &key (srl *current-srl*))
+ "Return a list of urel for cui"
+ (let ((urels '())
+ (ls (format nil "select REL,CUI2,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI1=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'urel
+ :cui1 cui
+ :rel (nth 0 tuple)
+ :cui2 (ensure-integer (nth 1 tuple))
+ :rela (nth 2 tuple)
+ :sab (nth 3 tuple)
+ :sl (nth 4 tuple)
+ :mg (nth 5 tuple)
+ :pfstr2 (nth 6 tuple))
+ urels))
+ (nreverse urels)))
+
+(defun find-urel-cui2 (cui2 &key (srl *current-srl*))
+ "Return a list of urel for cui2"
+ (let ((urels '())
+ (ls (format nil "select REL,CUI1,RELA,SAB,SL,MG,KPFSTR2 from MRREL where CUI2=~d" cui2)))
+ (when srl
+ (string-append ls (format nil " and SRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'urel
+ :cui2 cui2
+ :rel (nth 0 tuple)
+ :cui1 (ensure-integer (nth 1 tuple))
+ :rela (nth 2 tuple)
+ :sab (nth 3 tuple)
+ :sl (nth 4 tuple)
+ :mg (nth 5 tuple)
+ :pfstr2 (nth 6 tuple))
+ urels))
+ (nreverse urels)))
+
+(defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
+ (mapcar
+ #'(lambda (cui) (find-ucon-cui cui :key srl))
+ (remove-duplicates (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))))
+
+(defun find-ucoc-cui (cui &key (srl *current-srl*))
+ "Return a list of ucoc for cui"
+ (let ((ucocs '())
+ (ls (format nil "select CUI2,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI1=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (string-append ls " order by COF asc")
+ (dolist (tuple (mutex-sql-query ls))
+ (let ((cui2 (ensure-integer (nth 0 tuple))))
+ (when (zerop cui2)
+ (setq cui2 nil))
+ (push (make-instance 'ucoc :cui1 cui
+ :cui2 cui2
+ :soc (nth 1 tuple)
+ :cot (nth 2 tuple)
+ :cof (ensure-integer (nth 3 tuple))
+ :coa (nth 4 tuple)
+ :pfstr2 (nth 5 tuple))
+ ucocs)))
+ ucocs)) ;; akready ordered by SQL select
+
+(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
+ "Return a list of ucoc for cui2"
+ (let ((ucocs '())
+ (ls (format nil "select CUI1,SOC,COT,COF,COA,KPFSTR2 from MRCOC where CUI2=~d" cui2)))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (string-append ls " order by COF asc")
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'ucoc :cui1 (ensure-integer (nth 0 tuple))
+ :cui2 cui2
+ :soc (nth 1 tuple)
+ :cot (nth 2 tuple)
+ :cof (ensure-integer (nth 3 tuple))
+ :coa (nth 4 tuple)
+ :pfstr2 (nth 5 tuple))
+ ucocs))
+ ucocs)) ;; already ordered by SQL select
+
+(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
+ "List of ucon with co-occurance cui2"
+ (mapcar
+ #'(lambda (cui) (find-ucon-cui cui :key 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"
+ (let ((ulos '())
+ (ls (format nil "select ISN,FR,UN,SUI,SNA,SOUI from MRLO where CUI=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'ulo :isn (nth 0 tuple)
+ :fr (ensure-integer (nth 1 tuple))
+ :un (nth 2 tuple)
+ :sui (ensure-integer (nth 3 tuple))
+ :sna (nth 4 tuple)
+ :soui (nth 5 tuple))
+ ulos))
+ (nreverse ulos)))
+
+(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"
+ (let ((uatxs '())
+ (ls (format nil "select SAB,REL,ATX from MRATX where CUI=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'uatx :sab (nth 0 tuple)
+ :rel (nth 1 tuple)
+ :atx (nth 2 tuple))
+ uatxs))
+ (nreverse uatxs)))
+
+
+(defun find-uterm-cui (cui &key (srl *current-srl*))
+ "Return a list of uterm for cui"
+ (let ((uterms '())
+ (ls (format nil "select distinct LUI,LAT,TS,KLUILRL from MRCON where CUI=~d" cui)))
+ (when srl
+ (string-append ls (format nil " and KLUILRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'uterm :lui (ensure-integer (nth 0 tuple))
+ :cui cui
+ :lat (nth 1 tuple)
+ :ts (nth 2 tuple)
+ :lrl (ensure-integer (nth 3 tuple)))
+ uterms))
+ (nreverse uterms)))
+
+(defun find-uterm-lui (lui &key (srl *current-srl*))
+ "Return a list of uterm for lui"
+ (if (stringp lui)
+ (setq lui (parse-lui lui)))
+ (let ((uterms '())
+ (ls (format nil "select distinct CUI,LAT,TS,KLUILRL from MRCON where LUI=~d" lui)))
+ (when srl
+ (string-append ls (format nil " and KLUILRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'uterm :cui (ensure-integer (nth 0 tuple))
+ :lui lui
+ :lat (nth 1 tuple)
+ :ts (nth 2 tuple)
+ :lrl (ensure-integer (nth 3 tuple)))
+ uterms))
+ (nreverse uterms)))
+
+(defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
+ "Return single uterm for cui/lui"
+ (let ((ls (format nil "select LAT,TS,KLUILRL from MRCON where KCUILUI=~d limit 1" (make-cuilui cui lui))))
+ (when srl
+ (string-append ls (format nil " and KLUILRL <= ~d" srl)))
+ (gu:aif (car (mutex-sql-query ls))
+ (make-instance 'uterm :cui cui
+ :lui lui
+ :lat (nth 0 gu::it)
+ :ts (nth 1 gu::it)
+ :lrl (ensure-integer (nth 2 gu::it)))
+ nil)))
+
+(defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
+ "Return a list of ustr for cui/lui"
+ (declare (fixnum cui lui))
+ (let ((ustrs '())
+ (ls (format nil "select SUI,STT,STR,LRL from MRCON where KCUILUI=~d" (make-cuilui cui lui))))
+ (when srl
+ (string-append ls (format nil " and LRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (let* ((sui (ensure-integer (car tuple)))
+ (ustr (make-instance 'ustr :sui sui
+ :cui cui
+ :cuisui (make-cuisui cui sui)
+ :lui lui
+ :stt (nth 1 tuple)
+ :str (nth 2 tuple)
+ :lrl (ensure-integer (nth 3 tuple)))))
+ (push ustr ustrs)))
+ (nreverse ustrs)))
+
+(defun find-ustr-cuisui (cui sui &key (srl *current-srl*))
+ "Return the single ustr for cuisui"
+ (let ((ls (format nil "select LUI,STT,STR,LRL from MRCON where KCUISUI=~d"
+ (make-cuisui cui sui))))
+ (when srl
+ (string-append ls (format nil " and LRL <= ~d" srl)))
+ (gu:aif (car (mutex-sql-query ls))
+ (make-instance 'ustr :sui sui
+ :cui cui
+ :cuisui (make-cuisui cui sui)
+ :lui (ensure-integer (nth 0 gu::it))
+ :stt (nth 1 gu::it)
+ :str (nth 2 gu::it)
+ :lrl (ensure-integer (nth 3 gu::it)))
+ nil)))
+
+(defun find-ustr-sui (sui &key (srl *current-srl*))
+ "Return the list of ustr for sui"
+ (if (stringp sui)
+ (setq sui (parse-sui sui)))
+ (let ((ustrs '())
+ (ls (format nil "select CUI,LUI,STT,STR,LRL from MRCON where SUI=~d" sui)))
+ (when srl
+ (string-append ls (format nil " and LRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (let ((cui (ensure-integer (car tuple))))
+ (push (make-instance 'ustr :sui sui
+ :cui cui
+ :cuisui (make-cuisui cui sui)
+ :lui (ensure-integer (nth 1 tuple))
+ :stt (nth 2 tuple)
+ :str (nth 3 tuple)
+ :lrl (ensure-integer (nth 4 tuple)))
+ ustrs)))
+ (nreverse ustrs)))
+
+(defun find-ustr-sab (sab &key (srl *current-srl*))
+ "Return the list of ustr for sab"
+ (let ((ustrs '())
+ (ls (format nil "select KCUISUI from MRSO where SAB='~a'" sab)))
+ (when srl
+ (string-append ls (format nil " and SRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (let ((cuisui (ensure-integer (car tuple))))
+ (push (apply #'find-ustr-cuisui
+ (append
+ (multiple-value-list (decompose-cuisui cuisui))
+ (list :srl srl)))
+ ustrs)))
+ (nreverse ustrs)))
+
+(defun find-ustr-all (&key (srl *current-srl*))
+ "Return list of all ustr's"
+ (let ((ls "select distinct CUI,LUI,SUI,STT,LRL,KPFSTR from MRCON"))
+ (when srl
+ (string-append ls (format nil " where LRL <= ~d" srl)))
+ (string-append ls " order by SUI asc")
+ (with-sql-connection (db)
+ (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))
+ ls
+ :database db))))
+
+(defun find-string-sui (sui &key (srl *current-srl*))
+ "Return the string associated with sui"
+ (let ((ls (format nil "select STR from MRCON where SUI=~d" sui)))
+ (when srl
+ (string-append ls (format nil " and LRL <= ~d" srl)))
+ (string-append ls " limit 1")
+ (caar (mutex-sql-query ls))))
+
+(defun find-uso-cuisui (cui sui &key (srl *current-srl*))
+ (declare (fixnum cui sui))
+ (let ((usos '())
+ (ls (format nil "select SAB,CODE,SRL,TTY from MRSO where KCUISUI=~d"
+ (make-cuisui cui sui))))
+ (when srl
+ (string-append ls (format nil " and SRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'uso :sab (nth 0 tuple) :code (nth 1 tuple)
+ :srl (nth 2 tuple) :tty (nth 3 tuple))
+ usos))
+ (nreverse usos)))
+
+(defun find-ucxt-cuisui (cui sui &key (srl *current-srl*))
+ (declare (fixnum cui sui))
+ (let ((ucxts '())
+ (ls (format nil "select SAB,CODE,CXN,CXL,RNK,CXS,CUI2,HCD,RELA,XC from MRCXT where KCUISUI=~d"
+ (make-cuisui cui sui))))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'ucxt :sab (nth 0 tuple)
+ :code (nth 1 tuple)
+ :cxn (ensure-integer (nth 2 tuple))
+ :cxl (nth 3 tuple)
+ :rnk (ensure-integer (nth 4 tuple))
+ :cxs (nth 5 tuple)
+ :cui2 (ensure-integer (nth 6 tuple))
+ :hcd (nth 7 tuple)
+ :rela (nth 8 tuple)
+ :xc (nth 9 tuple))
+ ucxts))
+ (nreverse ucxts)))
+
+(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 ")))
+ (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))))
+ (when srl
+ (string-append ls (format nil " and KSRL <= ~d" srl)))
+ (let ((usats '()))
+ (dolist (tuple (mutex-sql-query ls))
+ (push (make-instance 'usat :code (nth 0 tuple)
+ :atn (nth 1 tuple)
+ :sab (nth 2 tuple)
+ :atv (nth 3 tuple))
+ usats))
+ (nreverse usats))))
+
+
+(defun find-pfstr-cui (cui)
+ (caar (mutex-sql-query (format nil "select KPFSTR from MRCON where CUI=~d limit 1" cui))))
+
+(defun find-usty-tui (tui)
+ "Find usty for tui"
+ (setq tui (parse-tui tui))
+ (gu:aif (car (mutex-sql-query
+ (format nil "select STY from MRSTY where TUI=~d limit 1" tui)))
+ (make-instance 'usty :tui tui :sty (nth 0 gu::it))
+ nil))
+
+(defun find-usty-sty (sty)
+ "Find usty for a sty"
+ (gu:aif (car (mutex-sql-query
+ (format nil "select TUI from MRSTY where STY='~a' limit 1" sty)))
+ (make-instance 'usty :tui (ensure-integer (nth 0 gu::it)) :sty sty)
+ nil))
+
+(defun find-usty-all ()
+ "Return list of usty's for all semantic types"
+ (let ((ustys '()))
+ (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
+ (push (find-usty-tui (nth 0 tuple)) ustys))
+ (nreverse ustys)))
+
+(defun find-usty_freq-all ()
+ (let ((usty_freqs '()))
+ (dolist (tuple (mutex-sql-query "select distinct TUI from MRSTY"))
+ (let* ((tui (car tuple))
+ (freq (ensure-integer
+ (caar (mutex-sql-query
+ (format nil "select count(*) from MRSTY where TUI=~a" tui))))))
+ (push (make-instance 'usty_freq :usty (find-usty-tui tui) :freq freq) usty_freqs)))
+ (sort usty_freqs #'> :key #'usty_freq-freq)))
+
+
+
+
+(defun find-cui-max ()
+ (let ((cui (caar (mutex-sql-query "select max(CUI) from MRCON"))))
+ (ensure-integer cui)))
+
+;;;; Cross table find functions
+
+(defun find-ucon-tui (tui &key (srl *current-srl*))
+ "Find list of ucon for tui"
+ (when (stringp tui)
+ (setq tui (parse-tui tui)))
+ (let ((ucons '())
+ (ls (format nil "select CUI from MRSTY where TUI=~d" tui)))
+ (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 (ensure-integer (car tuple)) :srl srl) ucons))
+ ucons))
+
+(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))
+
+(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))
+
+(defun find-ustr-word (word &key (srl *current-srl*))
+ "Return list of ustrs that match word"
+ (let ((ustrs '())
+ (ls (format nil "select cui,sui from MRXW_ENG where wd='~a'" word)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (string-append ls " order by cui desc,sui desc")
+ (dolist (tuple (mutex-sql-query ls))
+ (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
+ ustrs))
+ ustrs))
+
+(defun find-ustr-normalized-word (word &key (srl *current-srl*))
+ "Return list of ustrs that match word"
+ (let ((ustrs '())
+ (ls (format nil "select cui,sui from MRXNW_ENG where nwd='~a'" word)))
+ (when srl
+ (string-append ls (format nil " and KLRL <= ~d" srl)))
+ (string-append ls " order by cui desc,sui desc")
+ (dolist (tuple (mutex-sql-query ls))
+ (push (find-ustr-cuisui (ensure-integer (car tuple)) (ensure-integer (cadr tuple)) :srl srl)
+ ustrs))
+ ustrs))
+
+
+;;; 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-ucon-normalized-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 '())
+ (nwords '()))
+ (dolist (word words)
+ (let ((nws (lvg:process-terms word)))
+ (dolist (nword nws)
+ (push nword nwords))))
+ (dolist (word nwords)
+ (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 find-ustr-normalized-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 '())
+ (nwords '()))
+ (dolist (word words)
+ (let ((nws (lvg:process-terms word)))
+ (dolist (nword nws)
+ (push nword nwords))))
+ (dolist (word nwords)
+ (setq ustrs (append ustrs (find-ustr-word word :srl srl))))
+ (sort-score-ustr-str str (delete-duplicates ustrs :test #'eql :key #'ustr-cui))))
+
+(defun a (str)
+ (find-normalized-matches-for-str str #'find-ustr-normalized-word #'ustr-sui))
+
+(defun find-normalized-matches-for-str (str lookup-func key-func)
+ "Return list of objects that normalize match for words in string,
+eliminate duplicates."
+ (let ((objs '())
+ (nwords '()))
+ (dolist (word (delimited-string-to-list str #\space))
+ (dolist (nword (lvg:process-terms word))
+ (unless (member nword nwords :test #'string-equal)
+ (push nword nwords))))
+ (dolist (nw nwords)
+ (setq objs (append objs (funcall lookup-func nw))))
+ (delete-duplicates objs :key key-func :test #'eql)))
+
+(defun sort-score-ucon-str (str ucons)
+ "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
+ (sort-score-umlsclass-str ucons 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))))
+
+(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))
+ (gu:aif (position (nth iword short-list) long-list :test #'string-equal)
+ (progn
+ (incf score (- 10 (abs (- gu::it iword))))
+ (decf unmatched))))
+ (decf score (* 2 unmatched))
+ score))
+
+
+;;; LEX SQL functions
+
+(defun find-lexterm-eui (eui)
+ (gu:awhen (car (mutex-sql-query
+ (format nil "select WRD from LRWD where EUI=~d" eui)))
+ (make-instance 'lexterm :eui eui :wrd (nth 0 gu:it))))
+
+(defun find-lexterm-word (wrd)
+ (gu:awhen (mutex-sql-query
+ (format nil "select EUI from LRWD where WRD='~a'" wrd))
+ (let ((terms '()))
+ (dolist (tuple gu:it)
+ (let ((eui (ensure-integer (nth 0 tuple))))
+ (push
+ (make-instance 'lexterm :eui eui :wrd (copy-seq wrd))
+ terms)))
+ (nreverse terms))))
+
+;; LEXTERM accessors, read on demand
+
+(def-lazy-reader lexterm s#abr find-labr-eui eui)
+(def-lazy-reader lexterm s#agr find-lagr-eui eui)
+(def-lazy-reader lexterm s#cmp find-lcmp-eui eui)
+(def-lazy-reader lexterm s#mod find-lmod-eui eui)
+(def-lazy-reader lexterm s#nom find-lnom-eui eui)
+(def-lazy-reader lexterm s#prn find-lprn-eui eui)
+(def-lazy-reader lexterm s#prp find-lprp-eui eui)
+(def-lazy-reader lexterm s#spl find-lspl-eui eui)
+(def-lazy-reader lexterm s#trm find-ltrm-eui eui)
+(def-lazy-reader lexterm s#typ find-ltyp-eui eui)
+
+;; LEX SQL Read functions
+
+(defun find-labr-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,ABR,EUI2,BAS2 from LRABR where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'labr :eui eui
+ :bas (nth 0 tuple)
+ :abr (nth 1 tuple)
+ :eui2 (ensure-integer (nth 2 tuple))
+ :bas2 (nth 3 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-labr-bas (bas)
+ (gu:awhen (mutex-sql-query
+ (format nil "select EUI,ABR,EUI2,BAS2 from LRABR where BAS='~a'" bas))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'labr :eui (ensure-integer (nth 0 tuple))
+ :bas (copy-seq bas)
+ :abr (nth 1 tuple)
+ :eui2 (ensure-integer (nth 2 tuple))
+ :bas2 (nth 3 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lagr-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select STR,SCA,AGR,CIT,BAS from LRAGR where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lagr
+ :eui eui
+ :str (nth 0 tuple)
+ :sca (nth 1 tuple)
+ :agr (nth 2 tuple)
+ :cit (nth 3 tuple)
+ :bas (nth 4 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lcmp-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,SCA,COM from LRCMP where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lcmp
+ :eui eui
+ :bas (nth 0 tuple)
+ :sca (nth 1 tuple)
+ :com (nth 2 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lmod-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,SCA,PSN_MOD,FEA from LRMOD where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lmod
+ :eui eui
+ :bas (nth 0 tuple)
+ :sca (nth 1 tuple)
+ :psnmod (nth 2 tuple)
+ :fea (nth 3 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lnom-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,SCA,EUI2,BAS2,SCA2 from LRNOM where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lnom
+ :eui eui
+ :bas (nth 0 tuple)
+ :sca (nth 1 tuple)
+ :eui2 (ensure-integer (nth 2 tuple))
+ :bas2 (nth 3 tuple)
+ :sca2 (nth 4 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lprn-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,NUM,GND,CAS,POS,QNT,FEA from LRPRN where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lprn
+ :eui eui
+ :bas (nth 0 tuple)
+ :num (nth 1 tuple)
+ :gnd (nth 2 tuple)
+ :cas (nth 3 tuple)
+ :pos (nth 4 tuple)
+ :qnt (nth 5 tuple)
+ :fea (nth 6 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lprp-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,STR,SCA,FEA from LRPRP where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lprp
+ :eui eui
+ :bas (nth 0 tuple)
+ :str (nth 1 tuple)
+ :sca (nth 2 tuple)
+ :fea (nth 3 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lspl-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select SPV,BAS from LRSPL where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'lspl
+ :eui eui
+ :spv (nth 0 tuple)
+ :bas (nth 1 tuple))
+ results))
+ (nreverse results))))
+
+
+(defun find-ltrm-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,GEN from LRTRM where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'ltrm
+ :eui eui
+ :bas (nth 0 tuple)
+ :gen (nth 1 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-ltyp-eui (eui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select BAS,SCA,TYP from LRTYP where EUI=~d" eui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'ltyp
+ :eui eui
+ :bas (nth 0 tuple)
+ :sca (nth 1 tuple)
+ :typ (nth 2 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-lwd-wrd (wrd)
+ (gu:awhen (mutex-sql-query
+ (format nil "select EUI from LRWD where WRD='~a'" wrd))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push (ensure-integer (nth 0 tuple)) results))
+ (make-instance 'lwd :wrd wrd
+ :euilist (nreverse results)))))
+
+;;; Semantic Network SQL access functions
+
+(defun find-sdef-ui (ui)
+ (gu:awhen (car (mutex-sql-query
+ (format nil "select RT,STY_RL,STN_RTN,DEF,EX,UN,RH,ABR,RIN from SRDEF where UI=~d" ui)))
+ (make-instance 'sdef :rt (nth 0 gu::it)
+ :ui ui
+ :styrl (nth 1 gu::it)
+ :stnrtn (nth 2 gu::it)
+ :def (nth 3 gu::it)
+ :ex (nth 4 gu::it)
+ :un (nth 5 gu::it)
+ :rh (nth 6 gu::it)
+ :abr (nth 7 gu::it)
+ :rin (nth 8 gu::it))))
+
+(defun find-sstre1-ui (ui)
+ (gu:awhen (mutex-sql-query
+ (format nil "select UI2,UI3 from SRSTRE1 where UI=~d" ui))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'sstre1 :ui ui
+ :ui2 (ensure-integer (nth 0 tuple))
+ :ui3 (ensure-integer (nth 1 tuple)))
+ results))
+ (nreverse results))))
+
+(defun find-sstre1-ui2 (ui2)
+ (gu:awhen (mutex-sql-query
+ (format nil "select UI,UI3 from SRSTRE1 where UI2=~d" ui2))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'sstre1 :ui (ensure-integer (nth 0 tuple))
+ :ui2 ui2
+ :ui3 (ensure-integer (nth 1 tuple)))
+ results))
+ (nreverse results))))
+
+(defun find-sstr-rl (rl)
+ (gu:awhen (mutex-sql-query
+ (format nil "select STY_RL,STY_RL2,LS from SRSTRE where RL='~a'" rl))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'sstr
+ :rl rl
+ :styrl (nth 0 tuple)
+ :styrl2 (nth 1 tuple)
+ :ls (nth 2 tuple))
+ results))
+ (nreverse results))))
+
+
+(defun find-sstre2-sty (sty)
+ (gu:awhen (mutex-sql-query
+ (format nil "select RL,STY2 from SRSTRE2 where STY='~a'" sty))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'sstre2
+ :sty (copy-seq sty)
+ :rl (nth 0 tuple)
+ :sty2 (nth 1 tuple))
+ results))
+ (nreverse results))))
+
+(defun find-sstr-styrl (styrl)
+ (gu:awhen (mutex-sql-query
+ (format nil "select RL,STY_RL2,LS from SRSTR where RL='~a'" styrl))
+ (let ((results '()))
+ (dolist (tuple gu::it)
+ (push
+ (make-instance 'sstr :styrl styrl
+ :rl (nth 0 tuple)
+ :styrl2 (nth 1 tuple)
+ :ls (nth 2 tuple))
+ results))
+ (nreverse results))))
+
+
;;;; -*- Mode: LISP; Syntax: Common-Lisp; Base: 10; Pkg: umlisp -*-
;; SQL/UMLS database Layer over database backend
;; Copyright (c) 2001 Kevin M. Rosenberg, M.D.
-;; $Id: sql.lisp,v 1.1 2002/10/05 20:17:14 kevin Exp $
+;; $Id: sql.lisp,v 1.2 2002/10/08 22:13:41 kevin Exp $
(in-package :umlisp)
(sql-disconnect-pooled)
(setq *umls-sql-dsn* dbname))
-(defvar *umls-sql-user* "webumls")
+(defvar *umls-sql-user* "secret")
(defun umls-sql-user ()
*umls-sql-user*)
(defun umls-sql-user! (u)
(sql-disconnect-pooled)
(setq *umls-sql-user* u))
-(defvar *umls-sql-passwd* "webumls")
+(defvar *umls-sql-passwd* "secret")
(defun umls-sql-passwd ()
*umls-sql-passwd*)
(defun umls-sql-passwd! (p)
;;;; -*- Mode: LISP; Syntax: ANSI-Common-Lisp; Base: 10 -*-
-;;;; $Id: umlisp.asd,v 1.1 2002/10/05 20:17:14 kevin Exp $
+;;;; $Id: umlisp.asd,v 1.2 2002/10/08 22:08:56 kevin Exp $
(in-package :asdf)
(:file "parse-macros" :depends-on ("sql"))
(:file "parse-2002" :depends-on ("parse-macros"))
(:file "parse-common" :depends-on ("parse-2002"))
- (:file "obj" :depends-on ("utils"))
- (:file "obj-sql" :depends-on ("obj" "sql"))
- (:file "obj-composite" :depends-on ("obj-sql"))))
+ (:file "classes" :depends-on ("utils"))
+ (:file "sql-classes" :depends-on ("classes" "sql"))
+ (:file "composite" :depends-on ("sql-classes"))))
projects / umlisp.git / commitdiff