(setq sqltype "VARCHAR2(20)")))))
(concatenate 'string
- (col c)
+ (sqlname c)
" "
(if (or (string-equal sqltype "VARCHAR")
(string-equal sqltype "CHAR"))
" MAX_ROWS=200000000"
"")
(if (eq *umls-sql-type* :mysql)
- " TYPE=MYISAM CHARACTER SET utf8"
+ " ENGINE=MYISAM CHARACTER SET utf8 COLLATE utf8_bin"
""))))
(defun create-custom-table-cmd (tablename sql-cmd)
(if (eql :mysql *umls-sql-type*)
(sql-execute "drop table if exists USRL" conn)
(ignore-errors (sql-execute "drop table USRL" conn)))
- (sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
+ (sql-execute
+ (concatenate 'string
+ "create table USRL (sab varchar(80), srl integer)"
+ (if (eq *umls-sql-type* :mysql)
+ " ENGINE=MYISAM CHARACTER SET utf8 COLLATE utf8_bin"
+ ""))
+ conn)
(dolist (tuple (mutex-sql-query
"select distinct SAB,SRL from MRCONSO order by SAB asc"))
(sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
(car tuple) (ensure-integer (cadr tuple)))
conn)))
+(defun make-ustats (conn)
+ (ignore-errors (sql-execute "drop table USTATS" conn))
+ (sql-execute
+ (concatenate 'string"create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)"
+ (if (eq *umls-sql-type* :mysql)
+ " ENGINE=MYISAM CHARACTER SET utf8 COLLATE utf8_bin"
+ ""))
+ 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)
+#+mrcoc (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 sql-create-special-tables (conn)
(make-usrl conn)
- (make-ustats))
+ (make-ustats conn))
(defun create-umls-db-by-insert (&key verbose)
"SQL Databases: initializes entire database via SQL insert commands"
(let ((translated-lines 0)
(input-lines 0)
(eof (cons nil nil)))
- (catch 'done-counting
- (with-open-file (ts output-path :direction :input
- #+(and sbcl sb-unicode) :external-format
- #+(and sbcl sb-unicode) :UTF-8
- #+(and allegro ics) :external-format
- #+(and allegro ics) :UTF-8
- #+lispworks :external-format
- #+lispworks :UTF-8
- #+(and clisp unicode) :external-format
- #+(and clisp unicode) charset:utf-8)
- (do ((c (read-char ts nil eof) (read-char ts nil eof)))
- ((eq c eof))
- (when (eql c #\newline)
- (incf translated-lines))))
- (dolist (input-ufile input-ufiles)
- (with-umls-ufile (line input-ufile)
- (incf input-lines)
- (when (> input-lines translated-lines)
- (throw 'done-counting 'incomplete)))))
+ (with-open-file (ts output-path :direction :input
+ #+(and sbcl sb-unicode) :external-format
+ #+(and sbcl sb-unicode) :UTF-8
+ #+(and allegro ics) :external-format
+ #+(and allegro ics) :UTF-8
+ #+lispworks :external-format
+ #+lispworks :UTF-8
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (do ((c (read-char ts nil eof) (read-char ts nil eof)))
+ ((eq c eof))
+ (when (eql c #\newline)
+ (incf translated-lines))))
+ (dolist (input-ufile input-ufiles)
+ (with-umls-ufile (line input-ufile)
+ (incf input-lines)
+ (when (> input-lines translated-lines)
+ (return))))
(cond
((< input-lines translated-lines)
(format t "Translated file ~A incomplete, deleting...~%" output-path)
(delete-file output-path)
nil)
((eql input-lines translated-lines)
- (format t "Translated file ~A already exists: skipping...~%" output-path)
+ (format t "Translated file ~A exists and is proper number of lines: skipping...~%" output-path)
t)
((eql input-lines 0)
(warn "The number of input lines is 0 for output file ~A." output-path)