X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=sql-classes.lisp;h=2831defc003504ff2c1f488793d013a80d612535;hb=9b9c48233072a8f64c9677d9b92b5eb956f4079d;hp=d38df6928f2281b8bdfff217b03dc8df58636ad6;hpb=6ebaa3627ee89b8f7f429ebcd01c4dc8d9892e0b;p=umlisp.git diff --git a/sql-classes.lisp b/sql-classes.lisp index d38df69..2831def 100644 --- a/sql-classes.lisp +++ b/sql-classes.lisp @@ -187,9 +187,21 @@ 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 + (format nil + "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A" + cui (if srl (format nil " AND SRL<=~D" srl) "")))))) + (unless tuple + (setq tuple (car (mutex-sql-query + (format nil + "SELECT kcuilrl,str FROM MRCONSO WHERE CUI=~D" + cui (if srl (format nil " AND SRL<=~D" srl) nil)))))) + (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 +213,45 @@ 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 DISTINCT str FROM MRCONSO WHERE CUI=~D AND KPFENG=1~A LIMIT 1" + cui (if srl (format nil " AND SRL<=~D" srl) "")))) + (caar (mutex-sql-query + (format nil "SELECT DISTINCT str FROM MRCONSO WHERE CUI=~D~A LIMIT 1" + cui (if srl (format nil " AND SRL<=~D" 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~A ORDER BY kcuilrl ASC LIMIT 1" + lui (if srl (format nil " AND SRL<=~D" srl) ""))))) + (unless tuple + (setq tuple (car (mutex-sql-query "SELECT cui,kcuilrl,str FROM MRCONSO WHERE LUI=~D~A ORDER BY kcuilrl ASC LIMIT 1" + lui (if srl (format nil " AND SRL<=~D" 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 +259,16 @@ 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 +277,20 @@ 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 +305,11 @@ 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 +357,12 @@ 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 +374,12 @@ 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 +390,25 @@ 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 +489,15 @@ 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))) @@ -697,33 +724,43 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS" ;;; Multiword lookup and score functions (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl - only-exact-if-match) + only-exact-if-match limit) (let ((uobjs '())) (dolist (word (delimited-string-to-list str #\space)) (setq uobjs (append uobjs (funcall obj-lookup-fun word :srl srl)))) (let ((sorted (funcall sort-fun str (delete-duplicates uobjs :test #'= :key key)))) - (if (and (plusp (length sorted)) - only-exact-if-match - (multiword-match str (pfstr (first sorted)))) - (first sorted) - sorted)))) + (let ((len (length sorted))) + (cond + ((zerop len) + (return-from find-uobj-multiword nil)) + ((and only-exact-if-match (multiword-match str (pfstr (first sorted)))) + (first sorted)) + (limit + (if (and (plusp limit) (> len limit)) + (subseq sorted 0 limit) + limit)) + (t + sorted)))))) (defun find-ucon-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str - #'cui srl only-exact-if-match)) + #'cui srl only-exact-if-match limit)) (defun find-uterm-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str - #'lui srl only-exact-if-match)) + #'lui srl only-exact-if-match limit)) (defun find-ustr-multiword (str &key (srl *current-srl*) - (only-exact-if-match t)) + (only-exact-if-match t) + limit) (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str - #'sui srl only-exact-if-match)) + #'sui srl only-exact-if-match limit)) (defun sort-score-pfstr-str (str uobjs) "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr" @@ -867,11 +904,11 @@ 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)