;;;; *************************************************************************
;;;; 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
;;;;
;;;; $Id$
;;;;
,%%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")))))
(if where-name
(format nil
(typecase where-value
- (number "=~D")
+ (number "='~D'")
(null " is null")
(t
(if like " like '%~A%""='~A'")))
(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))))
(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))))
(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
(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))))
(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
(defun find-cui-ucon-all (&key (srl *current-srl*))
"Return list of CUIs for all ucons"
- (collect-umlisp-query (mrcon (cui) srl nil nil :order (cui asc)
+ (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
:distinct t)
cui))
(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)))
(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)))
(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))))
(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))))
"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
"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
(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)))
(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)
(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
(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" "*" "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))