r11485: more use of vff

diff --git a/parse-rrf.lisp b/parse-rrf.lisp
index e5536a979f44d87c49e03fcfee13d6400cf721a1..ef56f8516358913b292bb6f88473e28163ec18ef 100644 (file)
--- a/parse-rrf.lisp
+++ b/parse-rrf.lisp
@@ -38,6 +38,25 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
     ((= 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
@@ -88,30 +107,31 @@ 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")
-        (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
-            (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 (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 (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
@@ -188,35 +208,15 @@ 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")
 
-(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))))))))
-
 (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
-       (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
@@ -314,8 +314,8 @@ used in the United States. We create a new scale (SRLUS) where SRL to SRLUS mapp
                                                 (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)))))
+      #+nil  ("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