Change default SQL server host

[umlisp.git] / parse-rrf.lisp

diff --git a/parse-rrf.lisp b/parse-rrf.lisp
index 90a11fcc5a63e3e34843b68bd7ce6fd79f532993..5e28ed5ca8a9f82f6cb9c89233e6e677b4fdf5cd 100644 (file)
--- a/parse-rrf.lisp
+++ b/parse-rrf.lisp
@@ -8,10 +8,8 @@
 ;;;; Author:   Kevin M. Rosenberg
 ;;;; Created:  Apr 2000
 ;;;;
 ;;;; Author:   Kevin M. Rosenberg
 ;;;; Created:  Apr 2000
 ;;;;

-;;;; $Id$
-;;;;

 ;;;; This file, part of UMLisp, is
 ;;;; This file, part of UMLisp, is

-;;;;    Copyright (c) 2000-2006 by Kevin M. Rosenberg, M.D.
+;;;;    Copyright (c) 2000-2010 by Kevin M. Rosenberg, M.D.

 ;;;;
 ;;;; UMLisp users are granted the rights to distribute and use this software
 ;;;; as governed by the terms of the GNU General Public License.
 ;;;;
 ;;;; UMLisp users are granted the rights to distribute and use this software
 ;;;; as governed by the terms of the GNU General Public License.


@@ -26,17 +24,40 @@
 
 (declaim (inline srl-to-srlus))
 (defun srl-to-srlus (srl)
 
 (declaim (inline srl-to-srlus))
 (defun srl-to-srlus (srl)

-  "Convert the standard SRL category to one oriented for use in the United States.
-Specifically, SRL 4 in the USA has license restrictions between SRL 1 and 2 when
-used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapping is:
-(0->0, 1->1, 4->2, 2->3, 3->4)."
-  (declare (fixnum srl))
+  "Convert the standard SRL category to one oriented for use in the ~
+United States. Specifically, SRL 4 in the USA has license restrictions ~
+between SRL 1 and 2 when used in the United States. As of 2009AA, the
+SNOMED SRL changed from 4 to 9. So we create a new scale ~
+(SRLUS) where SRL to SRLUS mapping is: ~
+(0->0, 1->1, 4->2, 9->2, 2->3, 3->4)."
+  (declare (type (integer 0 100) srl))

   (cond
   (cond

+    ((<= srl 1) srl)

     ((= srl 4) 2)
     ((= srl 4) 2)

+    ((= srl 9) 2)

     ((= srl 2) 3)
     ((= srl 3) 4)
     (t srl)))
 
     ((= srl 2) 3)
     ((= srl 3) 4)
     (t srl)))
 

+(defvar *vff-position-hash* (make-hash-table :size 100 :test 'eq))
+
+(defmacro vff (filename fieldname record)
+  (let ((pos (gensym "POS-"))
+        (found (gensym "FOUND-"))
+        (key (kmrcl:ensure-keyword (concatenate 'string filename "^" fieldname))))
+    `(locally (declare (optimize (speed 3) (safety 0)))
+      (multiple-value-bind (,pos ,found) (gethash ,key *vff-position-hash*)
+        (declare (ignore ,found))
+        (if ,pos
+            (locally (declare (type (integer 0 100000) ,pos))
+              (nth ,pos ,record))
+            (let ((,pos (position-field-file ,filename ,fieldname)))
+              (unless ,pos
+                (error "Did not find fieldname ~A in filename ~A." ,fieldname ,filename))
+              (locally (declare (type (integer 0 100000) ,pos))
+                (setf (gethash ,key *vff-position-hash*) ,pos)
+                (nth ,pos ,record))))))))
+

 (let ((pfstr-hash nil)      ;; Preferred concept strings by CUI
       (cui-lrl-hash nil)    ;; LRL by CUI
       (lui-lrl-hash nil)    ;; LRL by LUI
 (let ((pfstr-hash nil)      ;; Preferred concept strings by CUI
       (cui-lrl-hash nil)    ;; LRL by CUI
       (lui-lrl-hash nil)    ;; LRL by LUI


@@ -65,18 +86,18 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
 
   (defun make-preparse-hash-table ()
     (if sui-lrl-hash
 
   (defun make-preparse-hash-table ()
     (if sui-lrl-hash

-       (clear-preparse-hash-tables)
+        (clear-preparse-hash-tables)

       (setf
       (setf

-         pfstr-hash (make-hash-table :size 1500000)
-         cui-lrl-hash (make-hash-table :size 1500000)
-         lui-lrl-hash (make-hash-table :size 5000000)
-         sui-lrl-hash (make-hash-table :size 6000000)
-         cuisui-lrl-hash (make-hash-table :size 6000000)
-         cui-lrlus-hash (make-hash-table :size 1500000)
-         lui-lrlus-hash (make-hash-table :size 5000000)
-         sui-lrlus-hash (make-hash-table :size 6000000)
-         cuisui-lrlus-hash (make-hash-table :size 6000000)
-         sab-srl-hash (make-hash-table :size 200 :test 'equal)
+          pfstr-hash (make-hash-table :size 1500000)
+          cui-lrl-hash (make-hash-table :size 1500000)
+          lui-lrl-hash (make-hash-table :size 5000000)
+          sui-lrl-hash (make-hash-table :size 6000000)
+          cuisui-lrl-hash (make-hash-table :size 6000000)
+          cui-lrlus-hash (make-hash-table :size 1500000)
+          lui-lrlus-hash (make-hash-table :size 5000000)
+          sui-lrlus-hash (make-hash-table :size 6000000)
+          cuisui-lrlus-hash (make-hash-table :size 6000000)
+          sab-srl-hash (make-hash-table :size 200 :test 'equal)

           sab-srlus-hash (make-hash-table :size 200 :test 'equal))))
 
   (defun ensure-preparse (&optional (force-read nil))
           sab-srlus-hash (make-hash-table :size 200 :test 'equal))))
 
   (defun ensure-preparse (&optional (force-read nil))


@@ -87,30 +108,31 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
       (declare (fixnum counter)
                (ignorable counter))
       (with-umls-file (line "MRCONSO.RRF")
       (declare (fixnum counter)
                (ignorable counter))
       (with-umls-file (line "MRCONSO.RRF")

-        (let* ((cui (parse-ui (nth 0 line)))
-               (lui (parse-ui (nth 3 line)))
-               (sui (parse-ui (nth 5 line)))
-               (sab (nth 11 line))
-               (srl (parse-integer (nth 15 line)))
-               (srlus (srl-to-srlus srl)))
+        (let* ((cui (parse-ui (vff "MRCONSO.RRF" "CUI" line)))
+               (lui (parse-ui (vff "MRCONSO.RRF" "LUI" line)))
+               (sui (parse-ui (vff "MRCONSO.RRF" "SUI" line)))
+               (sab (vff "MRCONSO.RRF" "SAB" line))
+               (srl (parse-integer (vff "MRCONSO.RRF" "SRL" line)))
+               (srlus (srl-to-srlus srl))
+               (cuisui (make-cuisui cui sui)))

           #+sbcl
           (when (= 0 (mod (incf counter) 100000)) (sb-ext:gc :full t))
 
           ;; pfstr deprecated by KPFENG field in MRCONSO
           #+nil
           (unless (gethash cui pfstr-hash)  ;; if haven't stored pfstr for cui
           #+sbcl
           (when (= 0 (mod (incf counter) 100000)) (sb-ext:gc :full t))
 
           ;; pfstr deprecated by KPFENG field in MRCONSO
           #+nil
           (unless (gethash cui pfstr-hash)  ;; if haven't stored pfstr for cui

-            (when (and (string-equal (nth 1 line) "ENG") ; LAT
-                       (string-equal (nth 2 line) "P") ; ts
-                       (string-equal (nth 4 line) "PF")) ; stt
-             (setf (gethash cui pfstr-hash) (nth 14 line))))
+            (when (and (string-equal (vff "MRCONSO.RRF" "LAT" line) "ENG")
+                       (string-equal (vff "MRCONSO.RRF" "TS" line) "P")
+                       (string-equal (vff "MRCONSO.RRF" "STT" line) "PF"))
+              (setf (gethash cui pfstr-hash) (vff "MRCONSO.RRF" "STR" 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 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)
+          (set-lrl-hash cuisui srl cuisui-lrl-hash)

           (set-lrl-hash cui srlus cui-lrlus-hash)
           (set-lrl-hash lui srlus lui-lrlus-hash)
           (set-lrl-hash sui srlus sui-lrlus-hash)
           (set-lrl-hash cui srlus cui-lrlus-hash)
           (set-lrl-hash lui srlus lui-lrlus-hash)
           (set-lrl-hash sui srlus sui-lrlus-hash)

-          (set-lrl-hash (make-cuisui cui sui) srlus cuisui-lrlus-hash)
+          (set-lrl-hash cuisui srlus cuisui-lrlus-hash)

           (multiple-value-bind (val found) (gethash sab sab-srl-hash)
             (declare (ignore val))
             (unless found
           (multiple-value-bind (val found) (gethash sab sab-srl-hash)
             (declare (ignore val))
             (unless found


@@ -144,7 +166,7 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
     (declare (type (or null fixnum) hash-lrl)
              (boolean found))
     (if (or (not found) (< srl hash-lrl))
     (declare (type (or null fixnum) hash-lrl)
              (boolean found))
     (if (or (not found) (< srl hash-lrl))

-       (setf (gethash key hash) srl))))
+        (setf (gethash key hash) srl))))

 
 ;; UMLS file and column structures
 ;;; SQL datatypes symbols
 
 ;; UMLS file and column structures
 ;;; SQL datatypes symbols


@@ -187,34 +209,15 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
   '(("KCON" "SELECT CUI,STR FROM MRCONSO WHERE STT='PF' AND TS='P' AND ISPREF='Y' AND LAT='ENG'"))
   "Custom tables to create")
 
   '(("KCON" "SELECT CUI,STR FROM MRCONSO WHERE STT='PF' AND TS='P' AND ISPREF='Y' AND LAT='ENG'"))
   "Custom tables to create")
 

-(defvar *vff-position-hash* (make-hash-table :size 100 :test 'eq))
-
-
-(defmacro vff (filename fieldname record)
-  (let ((pos (gensym "POS-"))
-        (found (gensym "FOUND-"))
-        (key (kmrcl:ensure-keyword (concatenate 'string filename "^" fieldname))))
-    `(locally (declare (optimize (speed 3) (size 0) (safety 0)))
-      (multiple-value-bind (,pos ,found) (gethash ,key *vff-position-hash*)
-        (if ,pos
-            (locally (declare (type (integer 0 100000) ,pos))
-              (nth ,pos ,record))
-            (let ((,pos (position-field-file ,filename ,fieldname)))
-              (unless ,pos
-                (error "Did not find fieldname ~A in filename ~A." ,fieldname ,filename))
-              (locally (declare (type (integer 0 100000) ,pos))
-                (setf (gethash ,key *vff-position-hash*) ,pos)
-                (nth ,pos ,record))))))))
-

 (defparameter +custom-cols+
     '(#+nil ("MRCONSO.RRF" "KPFSTR" "TEXT"
              (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)
 (defparameter +custom-cols+
     '(#+nil ("MRCONSO.RRF" "KPFSTR" "TEXT"
              (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)

-             (lambda (x) (pfstr-hash (parse-ui (nth 0 x)))))
+             (lambda (x) (pfstr-hash (parse-ui (vff "MRCONSO.RRF" "CUI" x)))))

       ;; Set to 1 if term is prefered term for english
       ("MRCONSO.RRF" "KPFENG" "TINYINT" 0
       ;; Set to 1 if term is prefered term for english
       ("MRCONSO.RRF" "KPFENG" "TINYINT" 0

-       (lambda (x)  (if (and (string-equal (nth 1 x) "ENG") ; LAT
-                             (string-equal (nth 2 x) "P") ; ts
-                             (string-equal (nth 4 x) "PF")) ; stt
+       (lambda (x)  (if (and (string-equal (vff "MRCONSO.RRF" "LAT" x) "ENG")
+                             (string-equal (vff "MRCONSO.RRF" "TS" x) "P")
+                             (string-equal (vff "MRCONSO.RRF" "STT" x) "PF"))

                       "1"
                       "0")))
       ("MRCONSO.RRF" "KCUISUI" "BIGINT" 0
                       "1"
                       "0")))
       ("MRCONSO.RRF" "KCUISUI" "BIGINT" 0


@@ -222,7 +225,7 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
                                                  (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
       ("MRCONSO.RRF" "KCUILUI" "BIGINT" 0
        (lambda (x) (write-to-string (make-cuilui (parse-ui (vff "MRCONSO.RRF" "CUI" x))
                                                  (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
       ("MRCONSO.RRF" "KCUILUI" "BIGINT" 0
        (lambda (x) (write-to-string (make-cuilui (parse-ui (vff "MRCONSO.RRF" "CUI" x))

-                                                 (parse-ui (vff "MRCONSO.RRF" "SUI" x))))))
+                                                 (parse-ui (vff "MRCONSO.RRF" "LUI" x))))))

       ("MRCONSO.RRF" "KCUILRL" "TINYINT" 0
        (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRCONSO.RRF" "CUI" x))))))
       ("MRCONSO.RRF" "KCUILRLUS" "TINYINT" 0
       ("MRCONSO.RRF" "KCUILRL" "TINYINT" 0
        (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRCONSO.RRF" "CUI" x))))))
       ("MRCONSO.RRF" "KCUILRLUS" "TINYINT" 0


@@ -243,14 +246,14 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
        (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
       ("MRSTY.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cui-lrlus (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
        (lambda (x) (write-to-string (cui-lrl (parse-ui (vff "MRSTY.RRF" "CUI" x))))))
       ("MRSTY.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cui-lrlus (parse-ui (vff "MRSTY.RRF" "CUI" x))))))

-      ("MRCOC.RRF" "KLRL" "TINYINT" 0
+      #+mrcoc ("MRCOC.RRF" "KLRL" "TINYINT" 0

        (lambda (x) (write-to-string
        (lambda (x) (write-to-string

-                   (max (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
-                        (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
-      ("MRCOC.RRF" "KLRLUS" "TINYINT" 0
+                    (max (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
+                         (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
+      #+mrcoc ("MRCOC.RRF" "KLRLUS" "TINYINT" 0

        (lambda (x) (write-to-string
        (lambda (x) (write-to-string

-                   (max (cui-lrlus (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
-                        (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))
+                    (max (cui-lrlus (parse-ui (vff "MRCOC.RRF" "CUI1" x)))
+                         (kmrcl:aif (cui-lrl (parse-ui (vff "MRCOC.RRF" "CUI2" x))) kmrcl::it 0)))))

       ("MRSAT.RRF" "KSRL" "TINYINT" 0
        (lambda (x) (write-to-string (sab-srl (vff "MRSAT.RRF" "SAB" x)))))
       ("MRSAT.RRF" "KSRLUS" "TINYINT" 0
       ("MRSAT.RRF" "KSRL" "TINYINT" 0
        (lambda (x) (write-to-string (sab-srl (vff "MRSAT.RRF" "SAB" x)))))
       ("MRSAT.RRF" "KSRLUS" "TINYINT" 0


@@ -281,39 +284,39 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
        (lambda (x) (write-to-string (sab-srlus (vff "MRDEF.RRF" "SAB" x)))))
       ("MRXW_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
        (lambda (x) (write-to-string (sab-srlus (vff "MRDEF.RRF" "SAB" x)))))
       ("MRXW_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui

-                                                (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))

       ("MRXW_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
       ("MRXW_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui

-                                                (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXW_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXW_ENG.RRF" "SUI" x)))))))

       ("MRXW_NONENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
       ("MRXW_NONENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui

-                                                (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))

       ("MRXW_NONENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
       ("MRXW_NONENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui

-                                                (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXW_NONENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXW_NONENG.RRF" "SUI" x)))))))

       ("MRXNW_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
       ("MRXNW_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui

-                                                (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))

       ("MRXNW_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
       ("MRXNW_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui

-                                                (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXNW_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXNW_ENG.RRF" "SUI" x)))))))

       ("MRXNS_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui
       ("MRXNS_ENG.RRF" "KLRL" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrl (make-cuisui

-                                                (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))

       ("MRXNS_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui
       ("MRXNS_ENG.RRF" "KLRLUS" "TINYINT" 0
        (lambda (x) (write-to-string (cuisui-lrlus (make-cuisui

-                                                (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
-                                                (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))
+                                                 (parse-ui (vff "MRXNS_ENG.RRF" "CUI" x))
+                                                 (parse-ui (vff "MRXNS_ENG.RRF" "SUI" x)))))))

 
 

-      #+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)))))
+      #+nil  ("MRREL.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRREL.RRF" "CUI2" x)))))
+      #+mrcoc  ("MRCOC.RRF" "KPFSTR2" "TEXT" 1024 (lambda (x) (pfstr-hash (parse-ui (vff "MRCOC.RRF" "CUI2" x)))))

 
       ("MRSAT.RRF" "KCUILUI" "BIGINT" 0
        (lambda (x) (write-to-string (make-cuilui
 
       ("MRSAT.RRF" "KCUILUI" "BIGINT" 0
        (lambda (x) (write-to-string (make-cuilui


@@ -347,19 +350,20 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
     "Custom columns to create.(filename, col, sqltype, value-func).")
 
 (defparameter +index-cols+
     "Custom columns to create.(filename, col, sqltype, value-func).")
 
 (defparameter +index-cols+

-    '(("CUI1" "MRCOC") ("CUI" "MRCONSO") ("LUI" "MRCONSO")
-      ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
-      ("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
-      ("SCUI" "MRCONSO")
-      ("CUI" "MRDEF")
-      ("CUI1" "MRREL") ("CUI2" "MRREL") ("SAB" "MRREL")
+  '( #+mrcoc ("CUI1" "MRCOC") #+mrcoc ("KLRL" "MRCOC") #+mrcoc ("KLRLUS" "MRCOC")
+    ("CUI" "MRCONSO") ("LUI" "MRCONSO")
+    ("SRL" "MRCONSO") ("KSRLUS" "MRCONSO") ("AUI" "MRCONSO") ("KPFENG" "MRCONSO")
+    ("SUI" "MRCONSO") ("SAUI" "MRCONSO") ("CODE" "MRCONSO")
+    ("SCUI" "MRCONSO")
+    ("CUI" "MRDEF")
+    ("CUI1" "MRREL") ("CUI2" "MRREL") ("SAB" "MRREL")

       ("RUI" "MRREL") ("AUI1" "MRREL") ("AUI2" "MRREL")
       ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
       ("METAUI" "MRSAT") ("ATN" "MRSAT")
       ("CUI" "MRSTY")  ("TUI" "MRSTY") ("CUI" "MRXNS_ENG")
       ("RUI" "MRREL") ("AUI1" "MRREL") ("AUI2" "MRREL")
       ("CUI" "MRSAT") ("LUI" "MRSAT") ("SUI" "MRSAT")
       ("METAUI" "MRSAT") ("ATN" "MRSAT")
       ("CUI" "MRSTY")  ("TUI" "MRSTY") ("CUI" "MRXNS_ENG")

-      ("AUI" "MRHIER") ("CUI" "MRHIER") ("CXN" "MRHIER") ("RELA" "MRHIER") ("PAUI" "MRHIER")
-      ("SAB" "MRHIER")
-      #+ignore ("NSTR" "MRXNS_ENG" 10)
+      ("AUI" "MRHIER") ("CUI" "MRHIER") ("CXN" "MRHIER") ("RELA" "MRHIER")
+      ("PAUI" "MRHIER") ("SAB" "MRHIER")
+      ("NSTR" "MRXNS_ENG" 255)

       ("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
       ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO")
       ("KCUILRL" "MRCONSO") ("KLUILRL" "MRCONSO") ("KSUILRL" "MRCONSO")
       ("CUI" "MRXNW_ENG") ("NWD" "MRXNW_ENG") ("WD" "MRXW_ENG")
       ("KCUISUI" "MRCONSO") ("KCUILUI" "MRCONSO")
       ("KCUILRL" "MRCONSO") ("KLUILRL" "MRCONSO") ("KSUILRL" "MRCONSO")


@@ -369,8 +373,8 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
       ("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
       ("KSRL" "MRDEF") ("KSRL" "MRRANK")("KSRL" "MRREL") ("KSRL" "MRSAT")
       ("KSRLUS" "MRDEF") ("KSRLUS" "MRRANK")("KSRLUS" "MRREL") ("KSRLUS" "MRSAT")
       ("KCUISUI" "MRXNS_ENG") ("KCUISUI" "MRXW_NONENG")
       ("KSRL" "MRDEF") ("KSRL" "MRRANK")("KSRL" "MRREL") ("KSRL" "MRSAT")
       ("KSRLUS" "MRDEF") ("KSRLUS" "MRRANK")("KSRLUS" "MRREL") ("KSRLUS" "MRSAT")

-      ("KLRL" "MRCOC") ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
-      ("KLRLUS" "MRCOC") ("KLRLUS" "MRSTY") ("KLRLUS" "MRXW_ENG") ("KLRLUS" "MRXNW_ENG")
+      ("KLRL" "MRSTY") ("KLRL" "MRXW_ENG") ("KLRL" "MRXNW_ENG")
+      ("KLRLUS" "MRSTY") ("KLRLUS" "MRXW_ENG") ("KLRLUS" "MRXNW_ENG")

       ("KLRL" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
       ("KLRLUS" "MRXNS_ENG") ("KLRLUS" "MRXW_NONENG")
       ;; LEX indices
       ("KLRL" "MRXNS_ENG") ("KLRL" "MRXW_NONENG")
       ("KLRLUS" "MRXNS_ENG") ("KLRLUS" "MRXW_NONENG")
       ;; LEX indices


@@ -384,8 +388,7 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
       ("RL" "SRSTR")
 
       ("SRL" "MRSAB") ("KSRLUS" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")
       ("RL" "SRSTR")
 
       ("SRL" "MRSAB") ("KSRLUS" "MRSAB") ("RSAB" "MRSAB") ("VSAB" "MRSAB") ("RCUI" "MRSAB")

-      ("VCUI" "MRSAB") ("LAT" "MRSAB") ("MAPSETCUI" "MRMAP")  ("MAPSETCUI" "MRSMAP")
-      ("CUI" "MRHIER"))
+      ("VCUI" "MRSAB") ("LAT" "MRSAB") ("MAPSETCUI" "MRMAP")  ("MAPSETCUI" "MRSMAP"))

   "Columns in files to index")
 
 
   "Columns in files to index")
 
 


@@ -408,29 +411,29 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
   (let ((cols '()))
     (with-umls-file (line "MRCOLS.RRF")
       (destructuring-bind (col des ref min av max fil dty) line
   (let ((cols '()))
     (with-umls-file (line "MRCOLS.RRF")
       (destructuring-bind (col des ref min av max fil dty) line

-       (push (make-ucol col des ref (parse-integer min) (read-from-string av)
-                        (parse-integer max) fil dty)
-             cols)))
+        (push (make-ucol col des ref (parse-integer min) (read-from-string av)
+                         (parse-integer max) fil dty)
+              cols)))

     (nreverse cols)))
 
 (defun gen-ucols-custom ()
 "Initialize umls columns for custom columns"
   (loop for customcol in +custom-cols+
     (nreverse cols)))
 
 (defun gen-ucols-custom ()
 "Initialize umls columns for custom columns"
   (loop for customcol in +custom-cols+

-       collect
-       (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 (compile nil (nth 4 customcol)))))
+        collect
+        (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 (compile nil (nth 4 customcol)))))

 
 (defun gen-ucols-generic (col-filename)
 "Initialize for generic (LEX/NET) columns"
   (let ((cols '()))
     (with-umls-file (line col-filename)
       (destructuring-bind (nam des ref fil) line
 
 (defun gen-ucols-generic (col-filename)
 "Initialize for generic (LEX/NET) columns"
   (let ((cols '()))
     (with-umls-file (line col-filename)
       (destructuring-bind (nam des ref fil) line

-       (setq nam (escape-column-name nam))
-       (dolist (file (delimited-string-to-list fil #\,))
-         (push
-          (make-ucol nam des ref nil nil nil file nil)
-          cols))))
+        (setq nam (escape-column-name nam))
+        (dolist (file (delimited-string-to-list fil #\,))
+          (push
+           (make-ucol nam des ref nil nil nil file nil)
+           cols))))

     (nreverse cols)))
 
 
     (nreverse cols)))
 
 


@@ -447,18 +450,15 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
   (let ((files '()))
     (with-umls-file (line files-filename)
       (destructuring-bind (fil des fmt cls rws bts) line
   (let ((files '()))
     (with-umls-file (line files-filename)
       (destructuring-bind (fil des fmt cls rws bts) line

-       (push (make-ufile
-              dir fil des
-              (parse-integer cls)
-              (parse-integer rws) (parse-integer bts)
-              (concatenate 'list (umls-field-string-to-list fmt)
-                           (custom-colnames-for-filename fil)))
-             files)))
+        (push (make-ufile
+               dir fil des
+               (parse-integer cls)
+               (parse-integer rws) (parse-integer bts)
+               (concatenate 'list (umls-field-string-to-list fmt)
+                            (custom-colnames-for-filename fil)))
+              files)))

     (nreverse files)))
 
 (defun gen-ufiles-custom ()
   (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"
     (nreverse files)))
 
 (defun gen-ufiles-custom ()
   (make-ufile "META" "MRXW_NONENG.RRF" "Custom NonEnglish Index"

-             5 0 0 (fields (find-ufile "MRXW_ENG.RRF"))))
-
-
-
+              5 0 0 (fields (find-ufile "MRXW_ENG.RRF"))))