rmeta slc scc srl tfr cfr cxty ttyl atnl lat cenc
curver sabin))
-(defclass uso (umlsclass)
- ((sab :value-type string :initarg :sab :reader sab :hyperlink find-usab-rsab)
- (code :value-type string :initarg :code :reader code)
- (tty :value-type string :initarg :tty :reader tty :hyperlink find-btty-tty)
- (srl :value-type fixnum :initarg :srl :reader srl))
- (:metaclass hyperobject-class)
- (:user-name "Source")
- (:default-print-slots sab code tty srl))
-
(defclass ucxt (umlsclass)
((sab :value-type string :initarg :sab :reader sab :hyperlink find-usab-rsab)
(code :value-type string :initarg :code :reader code)
(str :value-type cdata :initarg :str :reader str)
(lrl :value-type fixnum :initarg :lrl :reader lrl)
(stt :value-type string :initarg :stt :reader stt)
- (s#so :reader s#so :subobject (find-uso-cuisui cui sui))
+ (s#so :reader s#atom :subobject (find-uso-cuisui cui sui))
(s#sat :reader s#sat :subobject (find-usat-ui cui lui sui))
(s#cxt :reader s#cxt :subobject (find-ucxt-cuisui cui sui)))
(:metaclass hyperobject-class)
(:user-name "String")
(:default-print-slots sui stt lrl str))
+(defclass uso (umlsclass)
+ ((aui :value-type fixnum :initarg :aui :reader aui :print-formatter fmt-aui)
+ (cui :value-type fixnum :initarg :cui :reader cui :print-formatter fmt-cui
+ :hyperlink find-ucon-cui)
+ (sui :value-type fixnum :initarg :cui :reader sui :print-formatter fmt-sui
+ :hyperlink find-ucon-sui)
+ (saui :value-type string :initarg :saui :reader saui)
+ (sdui :value-type string :initarg :sdui :reader sdui)
+ (scui :value-type string :initarg :scui :reader scui)
+ (tty :value-type string :initarg :tty :reader tty :hyperlink find-btty-tty)
+ (sab :value-type string :initarg :sab :reader sab :hyperlink find-usab-rsab)
+ (code :value-type string :initarg :code :reader code)
+ (srl :value-type fixnum :initarg :srl :reader srl))
+ (:metaclass hyperobject-class)
+ (:user-name "Source")
+ (:default-print-slots aui sab code saui adui scui tty srl))
+
(defclass ulo (umlsclass)
((isn :value-type string :initarg :isn :reader isn)
(fr :value-type fixnum :initarg :fr :reader fr)
(:default-print-slots soc cot cof coa cui2 pfstr2))
-(defclass uatx (umlsclass)
- ((sab :value-type string :initarg :sab :reader sab)
- (rel :value-type string :initarg :rel :reader rel)
- (atx :value-type cdata :initarg :atx :reader atx))
- (:metaclass hyperobject-class)
- (:user-name "Associated Expression")
- (:default-print-slots sab rel atx))
-
(defclass ucon (umlsclass)
((cui :value-type fixnum :initarg :cui :reader cui :print-formatter fmt-cui
:hyperlink find-ucon-cui)
(pfstr :value-type cdata :initarg :pfstr :reader pfstr)
(s#def :reader s#def :subobject (find-udef-cui cui))
(s#sty :reader s#sty :subobject (find-usty-cui cui))
- (s#atx :reader s#atx :subobject (find-uatx-cui cui))
(s#lo :reader s#lo :subobject (find-ulo-cui cui))
(s#term :reader s#term :subobject (find-uterm-cui cui))
(s#sat :reader s#sat :subobject (find-usat-ui cui))
(string-equal sqltype "CHAR"))
(format nil "~a (~a)" sqltype (cmax c))
sqltype))))))
- (format nil "CREATE TABLE ~a (~{~a~^,~})" (table file)
- (mapcar col-func (ucols file)))))
+ (format nil "CREATE TABLE ~a (~{~a~^,~})~A"
+ (table file)
+ (mapcar col-func (ucols file))
+ (if (and (eq *umls-sql-type* :mysql)
+ (string-equal (table file) "MRCXT"))
+ " MAX_ROWS=200000000"
+ ""))))
(defun create-custom-table-cmd (tablename sql-cmd)
"Return SQL command to create a custom table"
(dolist (file *umls-files*)
(sql-execute (create-table-cmd file) conn)))
+#+ignore
+(defun sql-create-kcon-table (conn)
+ "Create concept table, one row per concept."
+ (ignore-errors (execute-command "DROP TABLE KCON" :database conn))
+ (execute-command
+ (format nil "CREATE TABLE KCON (CUI INTEGER, STR ~A, LRL ~A)"
+ (case *umls-sql-type*
+ (:oracle
+ (format nil "VARCHAR2(~D)"
+ (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)))
+ (t "TEXT"))
+ (case *umls-sql-type*
+ (:mysql "TINYINT")
+ ((:postgresql :postgresql-socket) "INT2")
+ (:oracle "NUMBER(2,0)")
+ (t "INTEGER")))
+ :database conn)
+ (dolist (tuple (query "select distinct cui from MRCONSO order by cui"
+ :database conn))
+ (let ((cui (car tuple)))
+ (execute-command
+ (format nil "INSERT into KCON VALUES (~D,'~A',~D)"
+ cui
+ (add-sql-quotes (pfstr-hash cui) )
+ (cui-lrl cui))
+ :database conn))))
+
(defun sql-create-custom-tables (conn)
"SQL Databases: create all custom tables"
+ ;;(sql-create-kcon-table conn)
(dolist (ct +custom-tables+)
(sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn)))
"Return postgresql copy statement for a file"
(format
nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
- (table file) (umls-pathname (fil file) extension)))
+ (table file) (ufile-pathname file extension)))
(defun mysql-copy-cmd (file extension &key local-file)
"Return mysql copy statement for a file"
nil
"LOAD DATA ~AINFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
(if local-file "LOCAL " "")
- (umls-pathname (fil file) extension) (table file)))
+ (ufile-pathname file extension) (table file)))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; From classes.lisp
#1=(#:umlsclass
#:ucon #:uterm #:ustr #:usrl #:uso #:ucxt #:urank #:udef #:usat #:usab #:ulo
- #:urel #:ucoc #:usty #:uatx #:uxw #:uxnw #:uxns
+ #:urel #:ucoc #:usty #:uxw #:uxnw #:uxns
#:lexterm #:labr #:lagr #:lcmp #:lmod #:lnom #:lprn #:lprp #:lspl #:ltrm
#:ltyp #:lwd #:sdef #:sstr #:sstre1 #:sstre2
#:sty #:tui #:def #:sab #:srl #:tty #:rank #:supres #:atn #:atv #:vcui
#:rl #:sty2 #:ui #:ui2 #:ui3 #:eui #:bas #:eui2 #:bas2
#:cui #:lui #:sui #:wd #:lat #:nstr :cuilist
#:rsab #:lat
- #:s#def #:s#sty #:s#term #:s#str #:s#atx #:s#lo #:s#sat #:s#rel #:s#coc
+ #:s#def #:s#sty #:s#term #:s#str #:s#lo #:s#sat #:s#rel #:s#coc
#:s#so #:s#cxt
#:pfstr #:pfstr2 #:lrl #:def #:ts #:cui1 #:cui2 #:rela #:sl #:mg #:rel
#:soc #:cot #:cof #:coa #:isn #:fr #:un #:sna #:soui #:hcd #:stt #:str
#:find-usty-sty
#:find-ulo-cui
#:suistr
- #:find-uatx-cui
#:print-umlsclass
#:find-ucon-cui
#:find-ucon-cui-sans-pfstr
(defun find-ucols-for-ufile (ufile)
"Returns list of umls-cols for a file structure"
(loop for colname in (fields ufile)
- collect (find-ucol colname (fil ufile))))
+ collect (find-ucol colname
+ (if (subdir ufile)
+ (concatenate 'string (subdir ufile) "/" (fil ufile))
+ (fil ufile)))))
(defun umls-field-string-to-list (fmt)
"Converts a comma delimited list of fields into a list of field names. Will
"Return datatype for column name"
(second (find colname +col-datatypes+ :key #'car :test #'string-equal)))
+(defun canonicalize-column-type (type)
+ (cond
+ ((string-equal type "SMALLINT")
+ (case *umls-sql-type*
+ (:mysql "SMALLINT")
+ ((:postgresql :postgresql-socket) "INT2")
+ (:oracle "NUMBER(5,0)")
+ (t "INTEGER")))
+ ((string-equal type "INTEGER")
+ (case *umls-sql-type*
+ (:mysql "INTEGER")
+ ((:postgresql :postgresql-socket) "INT4")
+ (:oracle "NUMBER(9,0)")
+ (t "INTEGER")))
+ ((string-equal type "BIGINT")
+ (case *umls-sql-type*
+ (:mysql "BIGINT")
+ ((:postgresql :postgresql-socket) "INT8")
+ (:oracle "NUMBER(38,0)")
+ (t "INTEGER")))
+ ((string-equal type "TEXT")
+ (case *umls-sql-type*
+ (:mysql "TEXT")
+ ((:postgresql :postgresql-socket) "TEXT")
+ (:oracle "VARCHAR2(3000)")
+ (t "VARCHAR(3000)")))
+ ((string-equal type "VARCHAR")
+ (case *umls-sql-type*
+ (:mysql "VARCHAR")
+ ((:postgresql :postgresql-socket) "VARCHAR")
+ (:oracle "VARCHAR2")
+ (t "VARCHAR")))
+ ((string-equal type "NUMERIC")
+ (case *umls-sql-type*
+ (:mysql "NUMERIC")
+ ((:postgresql :postgresql-socket) "NUMERIC")
+ (:oracle "NUMBER")
+ (t "NUMERIC")))
+ (t
+ type)))
+
(defun ensure-ucol-datatype (col datatype)
-"Add data type information to column"
+ "Add data type information to column"
(setf (datatype col) datatype)
(case datatype
- (sql-u (setf (sqltype col) "INTEGER"
+ (sql-u (setf (sqltype col) (canonicalize-column-type "INTEGER")
(parse-fun col) #'parse-ui
(quote-str col) ""))
- (sql-s (setf (sqltype col) "SMALLINT"
+ (sql-s (setf (sqltype col) (canonicalize-column-type "SMALLINT")
(parse-fun col) #'parse-integer
(quote-str col) ""))
- (sql-l (setf (sqltype col) "BIGINT"
+ (sql-l (setf (sqltype col) (canonicalize-column-type "BIGINT")
(parse-fun col) #'parse-integer
(quote-str col) ""))
- (sql-i (setf (sqltype col) "INTEGER"
+ (sql-i (setf (sqltype col) (canonicalize-column-type "INTEGER")
(parse-fun col) #'parse-integer
(quote-str col) ""))
- (sql-f (setf (sqltype col) "NUMERIC"
+ (sql-f (setf (sqltype col) (canonicalize-column-type "NUMERIC")
(parse-fun col) #'read-from-string
(quote-str col) ""))
- (t ; Default column type, optimized text storage
+ (t ; Default column type, optimized text storage
(setf (parse-fun col) #'add-sql-quotes
(quote-str col) "'")
(when (and (cmax col) (av col))
(if (> (cmax col) 255)
- (setf (sqltype col) "TEXT")
- (setf (sqltype col) "VARCHAR"))))))
+ (setf (sqltype col) (canonicalize-column-type "TEXT"))
+ (setf (sqltype col) (canonicalize-column-type "VARCHAR")))))))
(defun escape-column-name (name)
(substitute #\_ #\/ name))
(defvar *preparse-hash-init?* nil)
(eval-when (:compile-toplevel :load-toplevel :execute)
-(let ((pfstr-hash nil) ;;; Preferred concept strings by CUI
- (cui-lrl-hash nil) ;;; LRL by CUI
- (lui-lrl-hash nil) ;;; LRL by LUI
- (cuisui-lrl-hash nil) ;;; LRL by CUISUI
- (sab-srl-hash nil)) ;;; SRL by SAB
+(let ((pfstr-hash nil) ;; Preferred concept strings by CUI
+ (cui-lrl-hash nil) ;; LRL by CUI
+ (lui-lrl-hash nil) ;; LRL by LUI
+ (sui-lrl-hash nil) ;; LRL by SUI
+ (cuisui-lrl-hash nil) ;; LRL by CUISUI
+ (sab-srl-hash nil)) ;; SRL by SAB
(defun make-preparse-hash-table ()
- (if pfstr-hash
+ (if sui-lrl-hash
(progn
(clrhash pfstr-hash)
(clrhash cui-lrl-hash)
(clrhash lui-lrl-hash)
+ (clrhash sui-lrl-hash)
(clrhash cuisui-lrl-hash)
(clrhash sab-srl-hash))
(setf
pfstr-hash (make-hash-table :size 800000)
cui-lrl-hash (make-hash-table :size 800000)
lui-lrl-hash (make-hash-table :size 1500000)
+ sui-lrl-hash (make-hash-table :size 1500000)
cuisui-lrl-hash (make-hash-table :size 1800000)
sab-srl-hash (make-hash-table :size 100 :test 'equal))))
(setf (gethash cui pfstr-hash) (nth 14 line))))
(set-lrl-hash cui srl cui-lrl-hash)
(set-lrl-hash lui srl lui-lrl-hash)
+ (set-lrl-hash sui srl sui-lrl-hash)
(set-lrl-hash (make-cuisui cui sui) srl cuisui-lrl-hash)
(multiple-value-bind (val found) (gethash sab sab-srl-hash)
(declare (ignore val))
(unless found
(setf (gethash sab sab-srl-hash) srl))))))
- (defun pfstr-hash (cui)
- (gethash cui pfstr-hash))
+ (defun pfstr-hash (cui) (gethash cui pfstr-hash))
+ (defun cui-lrl (cui) (gethash cui cui-lrl-hash))
+ (defun lui-lrl (lui) (gethash lui lui-lrl-hash))
+ (defun sui-lrl (sui) (gethash sui sui-lrl-hash))
+ (defun sab-srl (sab) (aif (gethash sab sab-srl-hash) it 0))
+ (defun cuisui-lrl (cuisui) (gethash cuisui cuisui-lrl-hash))
- (defun cui-lrl (cui)
- (gethash cui cui-lrl-hash))
-
- (defun lui-lrl (lui)
- (gethash lui lui-lrl-hash))
-
- (defun cuisui-lrl (cuisui)
- (gethash cuisui cuisui-lrl-hash))
-
- (defun sab-srl (sab)
- (aif (gethash sab sab-srl-hash) it 0))
)) ;; closure
(defun set-lrl-hash (key lrl hash)
(defparameter +col-datatypes+
'(("AV" sql-f) ("BTS" sql-i) ("CLS" sql-i) ("COF" sql-i) ("CUI1" sql-u)
- ("AUI" sql-u) ("AUI1" sql-u) ("AUI2" sql-u)
+ ("AUI" sql-u) ("AUI1" sql-u) ("AUI2" sql-u) ("PCUI" sql-u)
+ ("PLUI" 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)
("RNK" sql-s) ("RWS" sql-i) ("SRL" sql-s) ("SUI" sql-u) ("TUI" sql-u)
("UI" sql-u) ("UI2" sql-u) ("UI3" sql-u)
;; New fields for 2002AD
("RCUI" sql-u) ("VCUI" sql-u) ("CFR" sql-i) ("TFR" sql-i)
+ ("MAPSETCUI" sql-u)
)
"SQL data types for each non-string column")
(defparameter +custom-tables+
nil
+ #+ignore
+ '(("KCON" "SELECT CUI,STR FROM MRCONSO WHERE STT='PF' AND TS='P' AND ISPREF='Y' AND LAT='ENG'"))
"Custom tables to create")
(defparameter +custom-cols+
- '(("MRCONSO.RRF" "KPFSTR" "TEXT" 1024
- (lambda (x) (pfstr-hash (parse-ui (nth 0 x)))))
+ '(("MRCONSO.RRF" "KPFSTR" "TEXT"
+ (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)
+ (lambda (x) (pfstr-hash (parse-ui (nth 0 x)))))
("MRCONSO.RRF" "KCUISUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 5 x))))))
("MRCONSO.RRF" "KCUILUI" "BIGINT" 0
(lambda (x) (write-to-string (make-cuilui (parse-ui (nth 0 x)) (parse-ui (nth 3 x))))))
- ("MRCONSO.RRF" "KCUILRL" "INTEGER" 0
- (lambda (x) (write-to-string (cui-lrl (parse-ui (nth 0 x))))))
- ("MRCONSO.RRF" "KLUILRL" "INTEGER" 0
+ ("MRCONSO.RRF" "KCUILRL" "SMALLINT" 0
+ (lambda (x) (write-to-string (lui-lrl (parse-ui (nth 0 x))))))
+ ("MRCONSO.RRF" "KLUILRL" "SMALLINT" 0
(lambda (x) (write-to-string (lui-lrl (parse-ui (nth 3 x))))))
+ ("MRCONSO.RRF" "KSUILRL" "SMALLINT" 0
+ (lambda (x) (write-to-string (sui-lrl (parse-ui (nth 5 x))))))
;; Deprecated, last in 2004AA -- skip index
#+ignore
- ("MRLO.RRF" "KLRL" "INTEGER" 0
+ ("MRLO.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string
(if (zerop (length (nth 4 x)))
(cui-lrl (parse-ui (nth 0 x)))
(cuisui-lrl (make-cuisui (parse-ui (nth 0 x)) (parse-ui (nth 4 x))))))))
- ("MRSTY.RRF" "KLRL" "INTEGER" 0
+ ("MRSTY.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cui-lrl (parse-ui (nth 0 x))))))
- ("MRCOC.RRF" "KLRL" "INTEGER" 0
+ ("MRCOC.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string
(max (cui-lrl (parse-ui (nth 0 x)))
(kmrcl:aif (cui-lrl (parse-ui (nth 1 x))) kmrcl::it 0)))))
- ("MRSAT.RRF" "KSRL" "INTEGER" 0
+ ("MRSAT.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 9 x)))))
- ("MRREL.RRF" "KSRL" "INTEGER" 0
+ ("MRREL.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 10 x)))))
- ("MRRANK.RRF" "KSRL" "INTEGER" 0
+ ("MRRANK.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 1 x)))))
- ("MRDEF.RRF" "KSRL" "INTEGER" 0
+ ("MRDEF.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 4 x)))))
- ("MRCXT.RRF" "KSRL" "INTEGER" 0
+ ("MRCXT.RRF" "KSRL" "SMALLINT" 0
(lambda (x) (write-to-string (sab-srl (nth 2 x)))))
- ("MRATX.RRF" "KSRL" "INTEGER" 0
- (lambda (x) (write-to-string (sab-srl (nth 1 x)))))
- ("MRXW_ENG.RRF" "KLRL" "INTEGER" 0
+ ("MRXW_ENG.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXW_NONENG.RRF" "KLRL" "INTEGER" 0
+ ("MRXW_NONENG.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXNW_ENG.RRF" "KLRL" "INTEGER" 0
+ ("MRXNW_ENG.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
- ("MRXNS_ENG.RRF" "KLRL" "INTEGER" 0
+ ("MRXNS_ENG.RRF" "KLRL" "SMALLINT" 0
(lambda (x) (write-to-string (cuisui-lrl (make-cuisui
(parse-ui (nth 2 x))
(parse-ui (nth 4 x)))))))
"Custom columns to create.(filename, col, sqltype, value-func).")
(defparameter +index-cols+
- '(("CUI" "MRATX") ("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
+ '(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
("SRL" "MRCONSO") ("AUI" "MRCONSO")
("SUI" "MRCONSO") ("CUI" "MRCXT") ("CUI" "MRDEF") ("CUI" "MRLO")
("CUI1" "MRREL") ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
("TUI" "MRSTY") ("CUI" "MRXNS_ENG")
#+ignore ("NSTR" "MRXNS_ENG" 10)
("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
- ("KCUISUI" "MRCON") ("KCUILUI" "MRCON") ("KCUILRL" "MRCON")
- ("KLUILRL" "MRCON") ("KCUISUI" "MRCXT")
- ("KCUISUI" "MRSO") ("KCUISUI" "MRSAT") ("KCUILUI" "MRSAT")
+ ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO") ("KCUILRL" "MRCONSO")
+ ("KLUILRL" "MRCONSO") ("KCUISUI" "MRCXT")
+ ("KCUISUI" "MRSAT") ("KCUILUI" "MRSAT")
("KCUISUI" "MRXW_ENG") ("KCUISUI" "MRXNW_ENG")
("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
- ("KSRL" "MRATX") ("KSRL" "MRCXT") ("KSRL" "MRDEF") ("KSRL" "MRRANK")
+ ("KSRL" "MRCXT") ("KSRL" "MRDEF") ("KSRL" "MRRANK")
("KSRL" "MRREL") ("KSRL" "MRSAT") ("KLRL" "MRCOC")
#+ignore ("KLRL" "MRLO") ;; deprecated
("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
(defparameter +custom-index-cols+
nil
#+ignore
- '(("CUI" "MRCONFULL") ("SAB" "MRCONFULL") ("TUI" "MRCONFULL"))
+ '(("CUI" "KCON") ("LRL" "KCON"))
"Indexes to custom tables")
;; File & Column functions
"Initialize umls columns for custom columns"
(loop for customcol in +custom-cols+
collect
- (make-ucol (nth 1 customcol) "" 0 0 0 (nth 3 customcol)
- (nth 0 customcol) nil :sqltype (nth 2 customcol)
+ (make-ucol (nth 1 customcol) "" 0 0 0 (eval (nth 3 customcol))
+ (nth 0 customcol) nil :sqltype (canonicalize-column-type (nth 2 customcol))
:custom-value-fun (nth 4 customcol))))
(defun gen-ucols-generic (col-filename)
(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)))
(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)
(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)
projects / umlisp.git / commitdiff