X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=sql-classes.lisp;h=550cb2c9ebe231c9f7400a3f7fc46019d65e74dc;hb=62ce365967f05ec6a2945a20cd5c45efb7b809e5;hp=1eef61cb4a8c48bcbff45c881e24b8c854d42f7b;hpb=466bf8726b602d58e4ad1a103d9c9b36077521a1;p=umlisp.git diff --git a/sql-classes.lisp b/sql-classes.lisp index 1eef61c..550cb2c 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -2,12 +2,12 @@ ;;;; ************************************************************************* ;;;; FILE IDENTIFICATION ;;;; -;;;; Name: sql-classes.lisp -;;;; Purpose: Routines for reading UMLS objects from SQL database -;;;; Author: Kevin M. Rosenberg -;;;; Date Started: Apr 2000 +;;;; Name: sql-classes.lisp +;;;; Purpose: Routines for reading UMLS objects from SQL database +;;;; Author: Kevin M. Rosenberg +;;;; Created: Apr 2000 ;;;; -;;;; $Id: sql-classes.lisp,v 1.92 2003/08/27 23:55:17 kevin Exp $ +;;;; $Id$ ;;;; ;;;; This file, part of UMLisp, is ;;;; Copyright (c) 2000-2003 by Kevin M. Rosenberg, M.D. @@ -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 +216,7 @@ 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)))) @@ -223,7 +225,7 @@ 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 +233,7 @@ 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 +242,40 @@ 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))) @@ -298,6 +307,13 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" :cui2 (ensure-integer cui2) :rela rela :sab sab :sl sl :mg mg :pfstr2 kpfstr2))) +(defun find-cui2-urel-cui (cui &key (srl *current-srl*)) + "Return a list of urel for cui" + (ensure-cui-integer cui) + (collect-umlisp-query (mrrel (cui2) srl cui1 + cui :lrl "KSRL") + cui2)) + (defun find-urel-cui2 (cui2 &key (srl *current-srl*)) "Return a list of urel for cui2" (ensure-cui-integer cui2) @@ -319,7 +335,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (collect-umlisp-query (mrcoc (cui2 soc cot cof coa kpfstr2) srl cui1 cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) - (when (zerop cui2) (setq cui2 nil)) + (when (eql 0 cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 cui :cui2 (ensure-integer cui2) :soc soc :cot cot :cof (ensure-integer cof) :coa coa :pfstr2 kpfstr2))) @@ -349,17 +365,11 @@ 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 +377,7 @@ 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 +386,7 @@ 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 +396,34 @@ 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 + (collect-umlisp-query (mrconso (sui stt str 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 - :lrl (ensure-integer lrl)))) + :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 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)))) + :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 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)))) + :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 +435,15 @@ 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 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)) + :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))) @@ -440,15 +451,23 @@ 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) @@ -466,13 +485,14 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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 @@ -497,12 +517,12 @@ 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) (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 @@ -510,13 +530,13 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-usab-by-key (key-name key) "Find usab for a key" - (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver mstart - mend imeta rmeta slc scc srl tfr cfr cxty + (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart + vend imeta rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc curver sabin) nil key-name key :single t) (make-instance 'usab :vcui (ensure-integer vcui) :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son - :sf sf :sver sver :mstart mstart :mend mend :imeta imeta + :sf sf :sver sver :vstart vstart :vend vend :imeta imeta :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl) :tfr (ensure-integer tfr) :cfr (ensure-integer cfr) :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc @@ -777,16 +797,15 @@ 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) + (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" "*" "LRL" srl) + (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "LRL" 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) @@ -831,11 +850,18 @@ 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))))