Update to UMLS 2014AB. Main change is removal of MRCOC.

[umlisp.git] / sql-classes.lisp

diff --git a/sql-classes.lisp b/sql-classes.lisp
index 87d59bfeff89409b1a11e710afd14869fc12c4f2..d1e19f3fea74dd3a36293dab1793f3b24250fad4 100644 (file)
--- a/sql-classes.lisp
+++ b/sql-classes.lisp
@@ -285,7 +285,8 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
 (defun find-uconso-sui (sui &key sab (srl *current-srl*))
   "Find uconso for a sui. If set SAB, the without-pfstr is on by default"
   (ensure-sui-integer sui)
-  (unless (and sui (stringp sab))
+;;  (unless (and sui (stringp sab))
+  (unless sui
     (return-from find-uconso-sui nil))
 
   (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
@@ -410,7 +411,8 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
 (defun find-udef-cui (cui &key (srl *current-srl*))
   "Return a list of udefs for cui"
   (ensure-cui-integer cui)
-  (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
+  (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL"
+                               :distinct t)
     (make-instance 'udef :sab sab :def def :suppress suppress)))
 
 (defun find-udoc-key (key)
@@ -493,7 +495,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                     (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
         collect (find-ucon-cui cui :srl srl)))
 
-(defun find-ucoc-cui (cui &key (srl *current-srl*))
+#+mrcoc (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) srl cui1
@@ -505,7 +507,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                    :cot cot :cof (ensure-integer cof) :coa coa :sab sab
                    :pfstr2 (find-pfstr-cui cui2))))
 
-(defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
+#+mrcoc (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) srl cui2
@@ -516,7 +518,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                    :sab sab :cot cot :cof (ensure-integer cof) :coa coa
                    :pfstr2 (find-pfstr-cui cui2))))
 
-(defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
+#+mrcoc (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
   "List of ucon with co-occurance cui2"
   (ensure-cui-integer cui2)
   (mapcar
@@ -555,7 +557,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
   (ensure-cui-integer cui)
   (ensure-lui-integer lui)
   (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
-                                 (make-cuilui cui lui) :lrl ksuilrl)
+                                 (make-cuilui cui lui) :lrl ksuilrl :distinct t)
                 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
                    :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
                    :lrl (ensure-integer ksuilrl))))
@@ -563,7 +565,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
 (defun find-ustr-cuisui (cuisui &key (srl *current-srl*))
   "Return the single ustr for cuisui"
   (collect-umlisp-query (mrconso (cui lui sui stt str suppress ksuilrl) srl kcuisui
-                                 cuisui :lrl lsuilrl :single t)
+                                 cuisui :lrl ksuilrl :single t)
     (make-instance 'ustr :sui sui :cui cui :cuisui cuisui
                    :lui (ensure-integer lui) :stt stt :str str :suppress suppress
                    :lrl (ensure-integer ksuilrl))))
@@ -578,7 +580,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
   "Return the list of ustr for sui"
   (ensure-sui-integer sui)
   (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
-                            :lrl ksuilrl)
+                            :lrl ksuilrl :distinct t)
     (make-instance 'ustr :sui sui :cui cui :stt stt :str str
                    :cuisui (make-cuisui (ensure-integer cui) sui)
                    :suppress suppress
@@ -1090,37 +1092,8 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
 ;;; **************************
 
 
-(defun make-ustats ()
-  (with-sql-connection (conn)
-    (ignore-errors (sql-execute "drop table USTATS" conn))
-    (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
-
-    (dolist (srl '(0 1 2 3 4 9))
-      (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 "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)
-      (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 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))
-    (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
-  (find-ustats-all))
-
-(defun insert-ustats-count (conn name table count-variable srl-control srl)
-  (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
-
 (defun find-count-table (conn table srl count-variable srl-control)
+  (with-sql-connection (conn)
   (cond
    ((stringp srl-control)
     (ensure-integer
@@ -1134,7 +1107,7 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
                       conn))))
    (t
     (error "Unknown srl-control")
-    0)))
+    0))))
 
 (defun insert-ustats (conn name count srl)
   (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
@@ -1157,4 +1130,3 @@ is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
 (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))))
-