X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=sql-classes.lisp;h=293c961b43157fb7d6af9c7fa97c696a0a325bf1;hb=b9fe7fe8b8e24133538f78dbaf6af73b5f0bdec2;hp=99634ca795afb47dc41b12e49bd65dd9be5c48a9;hpb=1a4bafb95bf16ef06c412cbc609c474941ae9924;p=umlisp.git diff --git a/sql-classes.lisp b/sql-classes.lisp index 99634ca..293c961 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -2,15 +2,15 @@ ;;;; ************************************************************************* ;;;; FILE IDENTIFICATION ;;;; -;;;; Name: sql-classes.lisp -;;;; Purpose: Routines for reading UMLS objects from SQL database -;;;; Author: Kevin M. Rosenberg -;;;; Date Started: Apr 2000 +;;;; Name: sql-classes.lisp +;;;; Purpose: Routines for reading UMLS objects from SQL database +;;;; Author: Kevin M. Rosenberg +;;;; Created: Apr 2000 ;;;; -;;;; $Id: sql-classes.lisp,v 1.91 2003/08/02 07:03:00 kevin Exp $ +;;;; $Id$ ;;;; ;;;; This file, part of UMLisp, is -;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D. +;;;; Copyright (c) 2000-2006 by Kevin M. Rosenberg, M.D. ;;;; ;;;; UMLisp users are granted the rights to distribute and use this software ;;;; as governed by the terms of the GNU General Public License. @@ -41,15 +41,16 @@ ,%%fields ,@(when %%where (list %%where)) ,@(when %%where - `((typecase ,where-value - (fixnum - (prefixed-fixnum-string ,where-value #\= 10)) - (number - (concatenate 'string "=" (write-to-string ,where-value))) - (null - " is null") - (t - (format nil ,(if like "'%~A%'" "='~A'") ,where-value))))) + `((typecase ,where-value + #+ignore + (fixnum + (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'")) + (number + (concatenate 'string "='" (write-to-string ,where-value) "'")) + (null + " is null") + (t + (format nil ,(if like "'%~A%'" "='~A'") ,where-value))))) (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "") ,@(when %%order (list %%order)) ,@(when single (list " limit 1"))))) @@ -64,7 +65,7 @@ (if where-name (format nil (typecase where-value - (number "=~D") + (number "='~D'") (null " is null") (t (if like " like '%~A%""='~A'"))) @@ -186,27 +187,28 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-cui (cui &key (srl *current-srl*)) "Find ucon for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcon (kpfstr kcuilrl) srl cui cui :single t) + (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl cui cui :single t) (make-instance 'ucon :cui cui :pfstr kpfstr :lrl (ensure-integer kcuilrl)))) (defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*)) "Find ucon for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcon (kcuilrl) srl cui cui :single t) + (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t) (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl) :pfstr nil))) (defun find-pfstr-cui (cui &key (srl *current-srl*)) "Find preferred string for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcon (kpfstr) srl cui cui :single t) + (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t) kpfstr)) + (defun find-ucon-lui (lui &key (srl *current-srl*)) "Find list of ucon for lui" (ensure-lui-integer lui) - (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl lui lui + (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui :distinct t) (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr :lrl (ensure-integer kcuilrl)))) @@ -214,7 +216,14 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-sui (sui &key (srl *current-srl*)) "Find list of ucon for sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl sui sui :distinct t) + (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr + :lrl (ensure-integer kcuilrl)))) + +(defun find-ucon-aui (aui &key (srl *current-srl*)) + "Find list of ucon for aui" + (ensure-sui-integer aui) + (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl aui aui :distinct t) (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr :lrl (ensure-integer kcuilrl)))) @@ -223,7 +232,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (ensure-cui-integer cui) (ensure-sui-integer sui) (when (and cui sui) - (collect-umlisp-query (mrcon (kpfstr kcuilrl) srl kcuisui + (collect-umlisp-query (mrconso (kpfstr kcuilrl) srl kcuisui (make-cuisui cui sui)) (make-instance 'ucon :cui cui :pfstr kpfstr @@ -231,7 +240,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucon-str (str &key (srl *current-srl*)) "Find ucon that are exact match for str" - (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl str str :distinct t) + (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t) (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr :lrl (ensure-integer kcuilrl)))) @@ -240,33 +249,40 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (with-sql-connection (db) (clsql:map-query 'list - #'(lambda (cui pfstr cuilrl) - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl))) - (query-string mrcon (cui kpfstr kcuilrl) srl nil nil + #'(lambda (tuple) + (destructuring-bind (cui pfstr cuilrl) tuple + (make-instance 'ucon :cui (ensure-integer cui) + :pfstr pfstr + :lrl (ensure-integer cuilrl)))) + (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t) :database db))) (defun find-ucon-all2 (&key (srl *current-srl*)) "Return list of all ucon's" - (collect-umlisp-query (mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t) (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr :lrl (ensure-integer kcuilrl)))) +(defun find-cui-ucon-all (&key (srl *current-srl*)) + "Return list of CUIs for all ucons" + (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc) + :distinct t) + cui)) + (defun map-ucon-all (fn &key (srl *current-srl*)) "Map a function over all ucon's" (with-sql-connection (db) (clsql:map-query nil - #'(lambda (cui pfstr cuilrl) - (funcall fn - (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl)))) - (query-string mrcon (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + #'(lambda (tuple) + (destructuring-bind (cui pfstr cuilrl) tuple + (funcall fn (make-instance 'ucon :cui (ensure-integer cui) + :pfstr pfstr + :lrl (ensure-integer cuilrl))))) + (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) :distinct t) :database db))) @@ -274,8 +290,30 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-udef-cui (cui &key (srl *current-srl*)) "Return a list of udefs for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrdef (sab def) srl cui cui :lrl "KSRL") - (make-instance 'udef :sab sab :def def))) + (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL") + (make-instance 'udef :sab sab :def def :suppress suppress))) + +(defun find-udoc-key (key) + "Return list of abbreviation documentation for a key" + (collect-umlisp-query (mrdoc (value type expl) nil dockey key) + (make-instance 'udoc :key key :value value :type type :expl expl))) + +(defun find-udoc-value (value) + "Return abbreviation documentation" + (collect-umlisp-query (mrdoc (dockey type expl) nil value value) + (make-instance 'udoc :key dockey :value value :type type :expl expl))) + +(defun find-udoc-key-value (key value) + (let ((tuple (car (mutex-sql-query + (format nil "SELECT TYPE,EXPL FROM MRDOC WHERE DOCKEY='~A' AND VALUE='~A'" + key value))))) + (when tuple + (make-instance 'udoc :key key :value value :type (first tuple) :expl (second tuple))))) + +(defun find-udoc-all () + "Return all abbreviation documentation" + (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil) + (make-instance 'udoc :key dockey :value value :type type :expl expl))) (defun find-usty-cui (cui &key (srl *current-srl*)) "Return a list of usty for cui" @@ -292,20 +330,29 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-urel-cui (cui &key (srl *current-srl*)) "Return a list of urel for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrrel (rel cui2 rela sab sl mg kpfstr2) srl cui1 - cui :lrl "KSRL") - (make-instance 'urel :cui1 cui :rel rel - :cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl - :mg mg :pfstr2 kpfstr2))) + (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf kpfstr2) + srl cui1 cui :lrl "KSRL") + (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel + :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2 + :rui rui :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir + :suppress suppress :cvf cvf :pfstr2 kpfstr2))) + +(defun find-cui2-urel-cui (cui &key (srl *current-srl*)) + "Return a list of urel for cui" + (ensure-cui-integer cui) + (collect-umlisp-query (mrrel (cui2) srl cui1 + cui :lrl "KSRL") + cui2)) (defun find-urel-cui2 (cui2 &key (srl *current-srl*)) "Return a list of urel for cui2" (ensure-cui-integer cui2) - (collect-umlisp-query (mrrel (rel cui1 rela sab sl mg kpfstr2) srl cui2 - cui2 :lrl "KSRL") - (make-instance 'urel :cui2 cui2 :rel rel - :cui1 (ensure-integer cui1) :rela rela :sab sab :sl sl - :mg mg :pfstr2 kpfstr2))) + (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf kpfstr2) + srl cui2 cui2 :lrl "KSRL") + (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2) :stype2 stype2 :rui rui :srui srui + :stype1 stype1 :cui1 (ensure-integer cui1) :aui1 (ensure-integer aui1) + :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf + :pfstr2 kpfstr2))) (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*)) (ensure-cui-integer cui2) @@ -316,22 +363,24 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-ucoc-cui (cui &key (srl *current-srl*)) "Return a list of ucoc for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1 + (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa kpfstr2) srl cui1 cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) - (when (zerop cui2) (setq cui2 nil)) - (make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2) - :soc soc :cot cot :cof (ensure-integer cof) :coa coa + (when (eql 0 cui2) (setq cui2 nil)) + (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1) + :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) + :cot cot :cof (ensure-integer cof) :coa coa :sab sab :pfstr2 kpfstr2))) (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*)) "Return a list of ucoc for cui2" (ensure-cui-integer cui2) - (collect-umlisp-query (mrcoc (cui1 soc cot cof coa kpfstr2) srl cui2 + (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa kpfstr2) srl cui2 cui2 :lrl klrl :order (cof asc)) (when (zerop cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2 - :soc soc :cot cot :cof (ensure-integer cof) :coa coa + :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2) + :sab sab :cot cot :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2))) (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*)) @@ -349,17 +398,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (make-instance 'ulo :isn isn :fr (ensure-integer fr) :un un :sui (ensure-integer sui) :sna sna :soui soui))) -(defun find-uatx-cui (cui &key (srl *current-srl*)) - "Return a list of uatx for cui" - (ensure-cui-integer cui) - (collect-umlisp-query (mratx (sab rel atx) srl cui cui :lrl ksrl) - (make-instance 'uatx :sab sab :rel rel :atx atx))) - (defun find-uterm-cui (cui &key (srl *current-srl*)) "Return a list of uterm for cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrcon (lui lat ts kluilrl) srl cui cui + (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui :lrl kluilrl :distinct t) (make-instance 'uterm :lui (ensure-integer lui) :cui cui :lat lat :ts ts :lrl (ensure-integer kluilrl)))) @@ -367,7 +410,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-uterm-lui (lui &key (srl *current-srl*)) "Return a list of uterm for lui" (ensure-lui-integer lui) - (collect-umlisp-query (mrcon (cui lat ts kluilrl) srl lui lui + (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui :lrl kluilrl :distinct t) (make-instance 'uterm :cui (ensure-integer cui) :lui lui :lat lat :ts ts :lrl (ensure-integer kluilrl)))) @@ -376,7 +419,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Return single uterm for cui/lui" (ensure-cui-integer cui) (ensure-lui-integer lui) - (collect-umlisp-query (mrcon (lat ts kluilrl) srl kcuilui + (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui (make-cuilui cui lui) :lrl kluilrl :single t) (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts @@ -386,34 +429,35 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" "Return a list of ustr for cui/lui" (ensure-cui-integer cui) (ensure-lui-integer lui) - (collect-umlisp-query (mrcon (sui stt str lrl) srl kcuilui - (make-cuilui cui lui) :lrl lrl) - (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui - :cuisui (make-cuisui cui sui) :stt stt :str str - :lrl (ensure-integer lrl)))) + (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui + (make-cuilui cui lui) :lrl ksuilrl) + (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui + :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress + :lrl (ensure-integer ksuilrl)))) (defun find-ustr-cuisui (cui sui &key (srl *current-srl*)) "Return the single ustr for cuisui" (ensure-cui-integer cui) (ensure-sui-integer sui) - (collect-umlisp-query (mrcon (lui stt str lrl) srl kcuisui - (make-cuisui cui sui) :lrl lrl :single t) + (collect-umlisp-query (mrconso (lui stt str suppress ksuilrl) srl kcuisui + (make-cuisui cui sui) :lrl lsuilrl :single t) (make-instance 'ustr :sui sui :cui cui :cuisui (make-cuisui cui sui) - :lui (ensure-integer lui) :stt stt :str str - :lrl (ensure-integer lrl)))) + :lui (ensure-integer lui) :stt stt :str str :suppress suppress + :lrl (ensure-integer ksuilrl)))) (defun find-ustr-sui (sui &key (srl *current-srl*)) "Return the list of ustr for sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrcon (cui lui stt str lrl) srl sui sui - :lrl lrl) + (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui + :lrl ksuilrl) (make-instance 'ustr :sui sui :cui cui :stt stt :str str :cuisui (make-cuisui (ensure-integer cui) sui) - :lui (ensure-integer lui) :lrl (ensure-integer lrl)))) + :suppress suppress + :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl)))) (defun find-ustr-sab (sab &key (srl *current-srl*)) "Return the list of ustr for sab" - (collect-umlisp-query (mrso (kcuisui) srl sab sab :lrl srl) + (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl) (let ((cuisui (ensure-integer kcuisui))) (apply #'find-ustr-cuisui (append @@ -425,14 +469,16 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (with-sql-connection (db) (clsql:map-query 'list - #'(lambda (cui lui sui stt lrl pfstr) - (make-instance 'ustr :cui (ensure-integer cui) - :lui (ensure-integer lui) :sui (ensure-integer sui) - :stt stt :str pfstr - :cuisui (make-cuisui (ensure-integer cui) - (ensure-integer sui)) - :lrl (ensure-integer lrl))) - (query-string mrcon (cui lui sui stt lrl kpfstr) srl nil nil :lrl lrl + #'(lambda (tuple) + (destructuring-bind (cui lui sui stt ksuilrl suppress pfstr) tuple + (make-instance 'ustr :cui (ensure-integer cui) + :lui (ensure-integer lui) :sui (ensure-integer sui) + :stt stt :str pfstr + :cuisui (make-cuisui (ensure-integer cui) + (ensure-integer sui)) + :suppress suppress + :lrl (ensure-integer ksuilrl)))) + (query-string mrconso (cui lui sui stt ksuilrl kpfstr) srl nil nil :lrl ksuilrl :distinct t :order (sui asc)) :database db))) @@ -440,39 +486,66 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-string-sui (sui &key (srl *current-srl*)) "Return the string associated with sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrcon (str) srl sui sui :lrl lrl :single t) + (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t) str)) (defun find-uso-cuisui (cui sui &key (srl *current-srl*)) (ensure-sui-integer sui) (ensure-cui-integer cui) - (collect-umlisp-query (mrso (sab code srl tty) srl kcuisui + (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui) srl kcuisui (make-cuisui cui sui) :lrl srl) - (make-instance 'uso :sab sab :code code :srl srl :tty tty))) + (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty + :cui cui :sui sui :saui saui :sdui sdui :scui scui))) + +(defun find-uso-aui (aui &key (srl *current-srl*)) + (ensure-sui-integer aui) + (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui) srl aui + aui :lrl srl :single t) + (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty + :sui sui :saui saui :sdui sdui :scui scui))) (defun find-ucxt-cuisui (cui sui &key (srl *current-srl*)) (ensure-cui-integer cui) (ensure-sui-integer sui) - (collect-umlisp-query (mrcxt (sab code cxn cxl rnk cxs cui2 hcd rela xc) + (collect-umlisp-query (mrcxt (sab rank code cxn cxl cxs cui2 hcd rela xc) srl kcuisui (make-cuisui cui sui) :lrl ksrl) - (make-instance 'ucxt :sab sab :code code + (make-instance 'ucxt :sab sab :code code + :rank rank :cxn (ensure-integer cxn) :cxl cxl :cxs cxs :hcd hcd - :rela rela :xc xc :rnk (ensure-integer rnk) + :rela rela :xc xc :cui2 (ensure-integer cui2)))) +(defun find-uhier-cui (cui &key (srl *current-srl*)) + (ensure-cui-integer cui) + (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf) + srl cui cui :lrl ksrl) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + +(defun find-uhier-all (&key (srl *current-srl*)) + (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf) + srl nil nil :lrl ksrl) + (make-instance 'uhier :cui cui :aui (ensure-integer aui) + :cxn (ensure-integer cxn) + :paui (ensure-integer paui) + :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf))) + (defun find-usat-ui (cui &optional (lui nil) (sui nil) &key (srl *current-srl*)) (ensure-cui-integer cui) (ensure-lui-integer lui) (ensure-sui-integer sui) (let ((ls "select CODE,ATN,SAB,ATV from MRSAT where ")) (cond - (sui (string-append ls "KCUISUI=" - (integer-string (make-cuisui cui sui) 14))) - (lui (string-append ls "KCUILUI=" + (sui (string-append ls "KCUISUI='" + (integer-string (make-cuisui cui sui) 14) + "'")) + (lui (string-append ls "KCUILUI='" (integer-string (make-cuilui cui lui) 14) - " and sui=0")) - (t (string-append ls "cui=" (prefixed-fixnum-string cui nil 7) - " and lui=0 and sui=0"))) + "' and sui='0'")) + (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7) + "' and lui='0' and sui='0'"))) (when srl (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3))) (loop for tuple in (mutex-sql-query ls) collect @@ -497,30 +570,32 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-usab-all () "Find usab for a key" - (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver mstart mend imeta + (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat - cenc curver sabin) nil nil nil) + cenc curver sabin ssn scit) nil nil nil) (make-instance 'usab :vcui (ensure-integer vcui) :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son - :sf sf :sver sver :mstart mstart :mend mend :imeta imeta + :sf sf :sver sver :vstart vstart :vend vend :imeta imeta :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl) :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc - :curver curver :sabin sabin))) + :curver curver :sabin sabin :ssn ssn :scit scit))) (defun find-usab-by-key (key-name key) "Find usab for a key" - (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver mstart - mend imeta rmeta slc scc srl tfr cfr cxty - ttyl atnl lat cenc curver sabin) - nil key-name key :single t) - (make-instance 'usab :vcui (ensure-integer vcui) - :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son - :sf sf :sver sver :mstart mstart :mend mend :imeta imeta - :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl) - :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) - :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc - :curver curver :sabin sabin))) + (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart + vend imeta rmeta slc scc srl tfr cfr cxty + ttyl atnl lat cenc curver sabin + ssn scit) + nil key-name key :single t) + (make-instance 'usab :vcui (ensure-integer vcui) + :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son + :sf sf :sver sver :vstart vstart :vend vend :imeta imeta + :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl) + :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) + :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc + :curver curver :sabin sabin + :ssn ssn :scit scit))) (defun find-usab-rsab (rsab) "Find usab for rsab" @@ -533,6 +608,20 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-cui-max () (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON")))) +(defun find-umap-cui (cui) + (ensure-cui-integer cui) + (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr + fromtype fromrule fromres rel rela toid tosid + toexpr totype torule tores maprule maptype + mapatn mapatv cvf) + nil mapsetcui cui) + (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid + :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid + :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres + :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype + :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn + :mapatv mapatv :cvf cvf))) + ;;;; Cross table find functions (defun find-ucon-tui (tui &key (srl *current-srl*)) @@ -735,9 +824,9 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ))) (defun find-lwd-wrd (wrd) - (make-instance 'lwd :wrd + (make-instance 'lwd :wrd wrd :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd) - (ensure-integer eui)))) + (ensure-integer eui)))) ;;; Semantic Network SQL access functions @@ -777,32 +866,28 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun make-ustats () (with-sql-connection (conn) - (sql-execute "drop table if exists USTATS" conn) + (ignore-errors (sql-execute "drop table USTATS" conn)) (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn) - (dotimes (srl 4) - (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) + (dotimes (srl 5) + (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl) + (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl) + (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl) + (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl) + (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl) (insert-ustats-count conn "Context Count" "MRCXT" "*" "KSRL" srl) (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl) (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl) + #+ignore (insert-ustats-count conn "Locator Count" "MRLO" "*" "KLRL" srl) (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl) (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl) (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl) (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl) - (insert-ustats-count conn "Source Count" "MRSO" "*" "SRL" srl) + (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl) (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl) (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl) - (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl) - (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)) + (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl)) (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn)) (find-ustats-all)) @@ -831,11 +916,18 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" conn)) (defun find-ustats-all (&key (srl *current-srl*)) - (collect-umlisp-query (ustats (name count srl) nil srl srl - :order (name asc)) - (make-instance 'ustats :name name :hits (ensure-integer count) - :srl (ensure-integer srl)))) - + (if srl + (collect-umlisp-query (ustats (name count srl) nil srl srl + :order (name asc)) + (make-instance 'ustats :name name + :hits (ensure-integer count) + :srl (ensure-integer srl))) + (collect-umlisp-query (ustats (name count srl) nil nil nil + :order (name asc)) + (make-instance 'ustats :name name + :hits (ensure-integer count) + :srl (ensure-integer srl))))) + (defun find-ustats-srl (srl) (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc)) (make-instance 'ustats :name name :hits (ensure-integer count))))