From: Kevin M. Rosenberg Date: Sat, 9 Sep 2006 19:47:58 +0000 (+0000) Subject: r11110: updates from old bdb repos X-Git-Tag: v2006ac.2~65 X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=commitdiff_plain;h=5a49f7c38351f819fe9b59f565f6e241aa2ffe0d r11110: updates from old bdb repos --- diff --git a/parse-rrf.lisp b/parse-rrf.lisp index c34f3ee..960653e 100644 --- a/parse-rrf.lisp +++ b/parse-rrf.lisp @@ -103,6 +103,7 @@ ("PLUI" sql-u) ("PAUI" sql-u) ("CUI2" sql-u) ("CUI" sql-u) ("CXN" sql-s) ("FR" sql-i) ("LRL" sql-s) ("LUI" sql-u) ("MAX" sql-s) ("MIN" sql-s) ("RANK" sql-s) ("REF" sql-c) + ("PTR" sql-c) ("RNK" sql-s) ("RWS" sql-i) ("SRL" sql-s) ("SUI" sql-u) ("TUI" sql-u) ("MAPRANK" sql-s) ;;; Custom columns @@ -159,6 +160,12 @@ (lambda (x) (write-to-string (sab-srl (nth 10 x))))) ("MRRANK.RRF" "KSRL" "SMALLINT" 0 (lambda (x) (write-to-string (sab-srl (nth 1 x))))) + ("MRHIER.RRF" "KSRL" "SMALLINT" 0 + (lambda (x) (write-to-string (sab-srl (nth 4 x))))) + ("MRMAP.RRF" "KSRL" "SMALLINT" 0 + (lambda (x) (write-to-string (sab-srl (nth 1 x))))) + ("MRSMAP.RRF" "KSRL" "SMALLINT" 0 + (lambda (x) (write-to-string (sab-srl (nth 1 x))))) ("MRDEF.RRF" "KSRL" "SMALLINT" 0 (lambda (x) (write-to-string (sab-srl (nth 4 x))))) #+nil ("MRCXT.RRF" "KSRL" "SMALLINT" 0 (lambda (x) (write-to-string (sab-srl (nth 2 x))))) @@ -179,11 +186,8 @@ (parse-ui (nth 2 x)) (parse-ui (nth 4 x))))))) - ;; FIXME: For MRREF and MRCOC, add lookups to KPFSTR2 using new MRCONSO index KPFENG - #+nil ("MRREL.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (nth 4 x))))) #+nil ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (nth 2 x))))) - #+use-mrctx ("MRCXT.RRF" "KCUISUI" "BIGINT" 0 (lambda (x) (write-to-string (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 1 x)))))) ("MRSAT.RRF" "KCUILUI" "BIGINT" 0 (lambda (x) (write-to-string (make-cuilui (parse-ui (nth 0 x)) (parse-ui (nth 1 x)))))) ("MRSAT.RRF" "KCUISUI" "BIGINT" 0 @@ -210,8 +214,7 @@ ("CUI1" "MRREL") ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT") ("CUI" "MRSTY") ("TUI" "MRSTY") ("CUI" "MRXNS_ENG") - ;; ("CUI" "MRCXT") ("KCUISUI" "MRCXT") ("KSRL" "MRCXT") - ("AUI" "MRHIER") ("PTR" "MRHIER") ("CUI" "MRHIER") ("CXN" "MRHIER") ("RELA" "MRHIER") ("PAUI" "MRHIER") + ("AUI" "MRHIER") ("PTR" "MRHIER" 255) ("CUI" "MRHIER") ("CXN" "MRHIER") ("RELA" "MRHIER") ("PAUI" "MRHIER") ("SAB" "MRHIER") #+ignore ("NSTR" "MRXNS_ENG" 10) ("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG") diff --git a/sql-classes.lisp b/sql-classes.lisp index d38df69..2c8c93e 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -187,9 +187,17 @@ 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 (mrconso (kpfstr kcuilrl) srl cui cui :single t) - (make-instance 'ucon :cui cui :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (unless cui (return-from find-ucon-cui nil)) + + (let ((tuple (car (mutex-sql-query "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND KPFENG=1 AND SRL<=~D" + cui srl)))) + (unless tuple + (setq tuple (car (mutex-sql-query "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND SRL<=~D" + cui srl)))) + (unless tuple + (return-from find-ucon-cui nil)) + (make-instance 'ucon :cui cui :pfstr (second tuple) + :lrl (ensure-integer (first tuple))))) (defun find-ucon-cui-sans-pfstr (cui &key (srl *current-srl*)) "Find ucon for a cui" @@ -201,30 +209,45 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (defun find-pfstr-cui (cui &key (srl *current-srl*)) "Find preferred string for a cui" (ensure-cui-integer cui) - (collect-umlisp-query (mrconso (kpfstr) srl cui cui :single t) - kpfstr)) - + (or + (caar (mutex-sql-query + (format nil "SELECT str FROM MRCONSO WHERE CUI=~D AND KPFENG=1 AND SLR<=~D" + cui srl))) + (caar (mutex-sql-query + (format nil "SELECT str FROM MRCONSO WHERE CUI=~D AND SLR<=~D" + cui srl))))) (defun find-ucon-lui (lui &key (srl *current-srl*)) "Find list of ucon for lui" (ensure-lui-integer lui) - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl lui lui + (collect-umlisp-query (mrconso (cui kcuilrl) srl lui lui :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr - :lrl (ensure-integer kcuilrl)))) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer kcuilrl))) + (unless lui (return-from find-ucon-lui nil)) + + (let ((tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D AND KPFENG=1 AND SRL<=~D" + lui srl)))) + (unless tuple + (setq tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D AND SRL<=~D" + lui srl)))) + (unless tuple + (return-from find-ucon-lui nil)) + (make-instance 'ucon :cui (first tuple) :pfstr (third tuple) + :lrl (ensure-integer (third tuple))))) (defun find-ucon-sui (sui &key (srl *current-srl*)) "Find list of ucon for sui" (ensure-sui-integer sui) - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl sui sui :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr + (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) :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 + (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-ucon-cuisui (cui sui &key (srl *current-srl*)) @@ -232,16 +255,16 @@ 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 (mrconso (kpfstr kcuilrl) srl kcuisui + (collect-umlisp-query (mrconso (kcuilrl) srl kcuisui (make-cuisui cui sui)) (make-instance 'ucon :cui cui - :pfstr kpfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl))))) (defun find-ucon-str (str &key (srl *current-srl*)) "Find ucon that are exact match for str" - (collect-umlisp-query (mrconso (cui kpfstr kcuilrl) srl str str :distinct t) - (make-instance 'ucon :cui (ensure-integer cui) :pfstr kpfstr + (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t) + (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-ucon-all (&key (srl *current-srl*)) @@ -250,20 +273,20 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query 'list #'(lambda (tuple) - (destructuring-bind (cui pfstr cuilrl) tuple + (destructuring-bind (cui cuilrl) tuple (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr - :lrl (ensure-integer cuilrl)))) - (query-string mrconso (cui kpfstr kcuilrl) srl nil nil + :pfstr (find-pfstr-cui cui) + :lrl (ensure-integer cuilrl)))) + (query-string mrconso (cui 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 (mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc) :distinct t) (make-instance 'ucon :cui (ensure-integer cui) - :pfstr kpfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer kcuilrl)))) (defun find-cui-ucon-all (&key (srl *current-srl*)) @@ -278,11 +301,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query nil #'(lambda (tuple) - (destructuring-bind (cui pfstr cuilrl) tuple + (destructuring-bind (cui cuilrl) tuple (funcall fn (make-instance 'ucon :cui (ensure-integer cui) - :pfstr pfstr + :pfstr (find-pfstr-cui cui) :lrl (ensure-integer cuilrl))))) - (query-string mrconso (cui kpfstr kcuilrl) srl nil nil :order (cui asc) + (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc) :distinct t) :database db))) @@ -330,12 +353,12 @@ 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 (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf kpfstr2) + (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) 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))) + :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2)))) (defun find-cui2-urel-cui (cui &key (srl *current-srl*)) "Return a list of urel for cui" @@ -347,12 +370,12 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf kpfstr2) + (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf) 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))) + :pfstr2 (find-pfstr-cui cui2)))) (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*)) (ensure-cui-integer cui2) @@ -363,25 +386,25 @@ 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 (aui1 cui2 aui2 sab cot cof coa kpfstr2) srl cui1 + (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1 cui :lrl klrl :order (cof asc)) (setq cui2 (ensure-integer cui2)) (when (eql 0 cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1) :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :cot cot :cof (ensure-integer cof) :coa coa :sab sab - :pfstr2 kpfstr2))) + :pfstr2 (find-pfstr-cui cui2)))) (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 aui1 aui2 sab cot cof coa kpfstr2) srl cui2 + (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2 cui2 :lrl klrl :order (cof asc)) (when (zerop cui2) (setq cui2 nil)) (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2) :sab sab :cot cot :cof (ensure-integer cof) :coa coa - :pfstr2 kpfstr2))) + :pfstr2 (find-pfstr-cui cui2)))) (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*)) "List of ucon with co-occurance cui2" @@ -462,15 +485,15 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (clsql:map-query 'list #'(lambda (tuple) - (destructuring-bind (cui lui sui stt ksuilrl suppress pfstr) tuple + (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple (make-instance 'ustr :cui (ensure-integer cui) :lui (ensure-integer lui) :sui (ensure-integer sui) - :stt stt :str pfstr + :stt stt :str (find-pfstr-cui cui) :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 + (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl :distinct t :order (sui asc)) :database db))) @@ -867,11 +890,11 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" (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 "Hierarchcy" "MRHIER" "*" "KSRL" srl) + (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl) + (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "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)