(let ((col-func
(lambda (c)
(let ((sqltype (sqltype c)))
+ (case *umls-sql-type*
+ (:oracle
+ (cond
+ ((string-equal sqltype "VARCHAR")
+ (setq sqltype "VARCHAR2"))
+ ((string-equal sqltype "BIGINT")
+ (setq sqltype "VARCHAR2(20)")))))
+
(concatenate 'string
- (col c)
- " "
- (if (or (string-equal sqltype "VARCHAR")
- (string-equal sqltype "CHAR"))
- (format nil "~a (~a)" sqltype (cmax c))
- sqltype))))))
- (format nil "CREATE TABLE ~a (~{~a~^,~})" (table file)
- (mapcar col-func (ucols file)))))
+ (col c)
+ " "
+ (if (or (string-equal sqltype "VARCHAR")
+ (string-equal sqltype "CHAR"))
+ (format nil "~a (~a)" sqltype (cmax c))
+ sqltype))))))
+ (format nil "CREATE TABLE ~a (~{~a~^,~})~A"
+ (table file)
+ (mapcar col-func (ucols file))
+ (if (and (eq *umls-sql-type* :mysql)
+ (string-equal (table file) "MRCXT"))
+ " MAX_ROWS=200000000"
+ ""))))
(defun create-custom-table-cmd (tablename sql-cmd)
"Return SQL command to create a custom table"
(defun noneng-lang-index-files ()
(remove-if-not
(lambda (f) (and (> (length (fil f)) 4)
- (string-equal (fil f) "MRXW." :end1 5)
- (not (string-equal (fil f) "MRXW.ENG"))
- (not (string-equal (fil f) "MRXW.NONENG"))))
+ (string-equal (fil f) "MRXW_" :end1 5)
+ (not (string-equal (fil f) "MRXW_ENG.RRF"))
+ (not (string-equal (fil f) "MRXW_NONENG.RRF"))))
*umls-files*))
;;; SQL Command Functions
(dolist (file *umls-files*)
(sql-execute (create-table-cmd file) conn)))
+#+ignore
+(defun sql-create-kcon-table (conn)
+ "Create concept table, one row per concept."
+ (ignore-errors (execute-command "DROP TABLE KCON" :database conn))
+ (execute-command
+ (format nil "CREATE TABLE KCON (CUI INTEGER, STR ~A, LRL ~A)"
+ (case *umls-sql-type*
+ (:oracle
+ (format nil "VARCHAR2(~D)"
+ (slot-value (find-ucol "STR" "MRCONSO.RRF") 'max)))
+ (t "TEXT"))
+ (case *umls-sql-type*
+ (:mysql "TINYINT")
+ ((:postgresql :postgresql-socket) "INT2")
+ (:oracle "NUMBER(2,0)")
+ (t "INTEGER")))
+ :database conn)
+ (dolist (tuple (query "select distinct cui from MRCONSO order by cui"
+ :database conn))
+ (let ((cui (car tuple)))
+ (execute-command
+ (format nil "INSERT into KCON VALUES (~D,'~A',~D)"
+ cui
+ (add-sql-quotes (pfstr-hash cui) )
+ (cui-lrl cui))
+ :database conn))))
+
(defun sql-create-custom-tables (conn)
"SQL Databases: create all custom tables"
+ ;;(sql-create-kcon-table conn)
(dolist (ct +custom-tables+)
(sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn)))
(sql-create-indexes conn +custom-index-cols+)
(sql-create-special-tables conn)))
-(defun create-umls-db (&optional (extension ".trans"))
+(defun create-umls-db (&key (extension ".trans") (skip-translation nil))
"SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
- (ignore-errors
- (clsql:destroy-database (list *umls-sql-host* (lookup-db-name *umls-sql-db*)
- *umls-sql-user* *umls-sql-passwd*)
- :database-type *umls-sql-type*))
- (clsql:create-database (list *umls-sql-host* (lookup-db-name *umls-sql-db*)
- *umls-sql-user* *umls-sql-passwd*)
- :database-type *umls-sql-type*)
(ensure-ucols+ufiles)
(ensure-preparse)
- (translate-all-files extension)
+ (unless skip-translation
+ (translate-all-files extension))
(let ((copy-cmd
(ecase (umls-sql-type)
(:mysql #'mysql-copy-cmd)
(:postgresql #'pg-copy-cmd))))
(with-sql-connection (conn)
+ (clsql:truncate-database :database conn)
(sql-drop-tables conn)
(sql-create-tables conn)
(dolist (file *umls-files*)
(defun translate-all-files (&optional (extension ".trans"))
"Copy translated files and return postgresql copy commands to import"
(make-noneng-index-file extension)
- (dolist (f (remove "MRXW.NONENG" *umls-files* :test #'string= :key #'fil))
+ (dolist (f (remove "MRXW_NONENG.RRF" *umls-files* :test #'string= :key #'fil))
(translate-umls-file f extension)))
(defun translate-umls-file (file extension)
(defun make-noneng-index-file (extension)
"Make non-english index file"
- (translate-files (find-ufile "MRXW.NONENG")
+ (translate-files (find-ufile "MRXW_NONENG.RRF")
extension (noneng-lang-index-files)))
(defun translate-files (out-ufile extension input-ufiles)
"Translate a umls file into a format suitable for sql copy cmd"
- (let ((output-path (umls-pathname (fil out-ufile) extension)))
+ (let ((output-path (ufile-pathname out-ufile extension)))
(if (probe-file output-path)
(format t "File ~A already exists: skipping~%" output-path)
(with-open-file (ostream output-path :direction :output)
(dolist (input-ufile input-ufiles)
- (with-umls-file (line (fil input-ufile))
+ (with-umls-ufile (line input-ufile)
(translate-line out-ufile line ostream)
(princ #\newline ostream)))))))
"Return postgresql copy statement for a file"
(format
nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
- (table file) (umls-pathname (fil file) extension)))
+ (table file) (ufile-pathname file extension)))
-(defun mysql-copy-cmd (file extension)
+(defun mysql-copy-cmd (file extension &key local-file)
"Return mysql copy statement for a file"
(format
nil
- "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
- (umls-pathname (fil file) extension) (table file)))
+ "LOAD DATA ~AINFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
+ (if local-file "LOCAL " "")
+ (ufile-pathname file extension) (table file)))
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projects / umlisp.git / blobdiff