Add support for MYSQL 8 with sqlname indirection to prevent reserved word collisions

[umlisp.git] / sql-classes.lisp

diff --git a/sql-classes.lisp b/sql-classes.lisp
index df23c492e224aae5812ddd15314655f4642534a1..2b468dc095080d61e621470005df128dbf1131b1 100644 (file)
--- a/sql-classes.lisp
+++ b/sql-classes.lisp
@@ -23,17 +23,31 @@
 (defun set-current-srl (srl)
   (setq *current-srl* srl))
 
+;; SQLNAME is required for collision of SQL reserved words (MYSQL 8: RANK)
+;; and column names in UMLS (RANK in MRRANK)
+(defvar *sql-reserved-names* '("RANK"))
+(defmethod sqlname ((c ucol))
+  (sqlname (col c)))
+(defmethod sqlname ((name string))
+  (if (find name *sql-reserved-names* :test #'string-equal)
+      (concatenate 'string "_" name)
+    name))
+(defmethod sqlname ((l list))
+  (mapcar #'sqlname l))
+(defmethod sqlname ((s symbol))
+  (sqlname (symbol-name s)))
+
 (defmacro query-string (table fields srl where-name where-value
                         &key (lrl "KCUILRL") single distinct order like limit
                         filter)
   (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
-                           (if distinct "DISTINCT " "") fields table))
+                           (if distinct "DISTINCT " "") (sqlname fields) table))
          (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}"
                                     order)
                       ""))
          (%%lrl (format nil " AND ~:@(~A~)<=" lrl))
          (%%where (when where-name
-                    (format nil " WHERE ~:@(~A~)~A" where-name
+                    (format nil " WHERE ~:@(~A~)~A" (sqlname where-name)
                           (if like " like " ""))))
          (%filter (gensym "FILTER-"))
          (%single (gensym "SINGLE-"))
@@ -77,8 +91,8 @@
   (concatenate
    'string
    (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
-           (if distinct "DISTINCT " "") fields table)
-   (if where-name (format nil " WHERE ~:@(~A~)" where-name) "")
+           (if distinct "DISTINCT " "") (sqlname fields) table)
+   (if where-name (format nil " WHERE ~:@(~A~)" (sqlname where-name)) "")
    (if where-name
        (format nil
                (typecase where-value
@@ -495,7 +509,7 @@ 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
@@ -507,7 +521,7 @@ 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
@@ -518,7 +532,7 @@ 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
@@ -1092,37 +1106,8 @@ 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
@@ -1136,7 +1121,7 @@ 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)"
@@ -1159,3 +1144,14 @@ 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))))
+
+(defun find-urank-sab (sab &key (srl *current-srl*))
+  (collect-umlisp-query (mrrank (rank sab suppress tty) nil sab sab)
+                        (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress)))
+
+(defun find-urank-all (&key (srl *current-srl*))
+  (if srl
+      (collect-umlisp-query (mrrank (rank sab suppress tty) nil ksrl srl)
+                            (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress))
+      (collect-umlisp-query (mrrank (rank sab suppress tty ksrl) nil nil nil)
+                            (make-instance 'urank :rank rank :sab sab :tty tty :suppress suppress))))