;;;; $Id$
;;;;
;;;; This file, part of UMLisp, is
-;;;; Copyright (c) 2000-2004 by Kevin M. Rosenberg, M.D.
+;;;; Copyright (c) 2000-2006 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.
(defun create-table-cmd (file)
"Return sql command to create a table"
- (let ((col-func
- (lambda (c)
+ (let ((col-func
+ (lambda (c)
(let ((sqltype (sqltype c)))
(case *umls-sql-type*
(:oracle
(setq sqltype "VARCHAR2"))
((string-equal sqltype "BIGINT")
(setq sqltype "VARCHAR2(20)")))))
-
+
(concatenate 'string
(col c)
" "
(string-equal sqltype "CHAR"))
(format nil "~a (~a)" sqltype (cmax c))
sqltype))))))
- (format nil "CREATE TABLE ~a (~{~a~^,~})~A"
+ (format nil "CREATE TABLE ~a (~{~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"
- ""))))
+ "")
+ (if (eq *umls-sql-type* :mysql)
+ " TYPE=MYISAM CHARACTER SET utf8"
+ ""))))
(defun create-custom-table-cmd (tablename sql-cmd)
"Return SQL command to create a custom table"
(format nil "CREATE TABLE ~a AS ~a;" tablename sql-cmd))
(defun insert-col-value (col value)
- (if (null (parse-fun col))
+ (if (null (parse-fun col))
value
(format nil "~A" (funcall (parse-fun col) value))))
(defun insert-values-cmd (file values)
- "Return sql insert command for a row of values"
+ "Return sql insert command for a row of values"
(let ((insert-func
(lambda (col value)
(concatenate 'string (quote-str col)
(table file)
(fields file)
(concat-separated-strings
- ","
+ ","
(mapcar insert-func (remove-custom-cols (ucols file)) values)
(custom-col-values (custom-ucols-for-file file) values t)))))
(defun noneng-lang-index-files ()
(remove-if-not
(lambda (f) (and (> (length (fil f)) 4)
- (string-equal (fil f) "MRXW_" :end1 5)
+ (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*))
"Return sql create index command"
(format nil "CREATE INDEX ~a ON ~a (~a)"
(concatenate 'string tablename "_" colname "_X")
- tablename
+ tablename
(case *umls-sql-type*
(:mysql
(concatenate 'string colname
(defun sql-drop-tables (conn)
"SQL Databases: drop all tables"
(dolist (file *umls-files*)
- (ignore-errors
+ (ignore-errors
(sql-execute (format nil "DROP TABLE ~a" (table file)) conn))))
(defun sql-create-tables (conn)
- "SQL Databases: create all tables"
+ "SQL Databases: create all tables"
(dolist (file *umls-files*)
(sql-execute (create-table-cmd file) conn)))
(:oracle "NUMBER(2,0)")
(t "INTEGER")))
:database conn)
+ ;; KCON deprecated by KPFENG field in MRCONSO
+ #+nil
(dolist (tuple (query "select distinct cui from MRCONSO order by cui"
:database conn))
(let ((cui (car tuple)))
- (execute-command
+ (execute-command
(format nil "INSERT into KCON VALUES (~D,'~A',~D)"
cui
(add-sql-quotes (pfstr-hash cui) )
;;(sql-create-kcon-table conn)
(dolist (ct +custom-tables+)
(sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn)))
-
+
(defun sql-insert-values (conn file)
- "SQL Databases: inserts all values for a file"
+ "SQL Databases: inserts all values for a file"
(with-umls-file (line (fil file))
(sql-execute (insert-values-cmd file line) conn)))
(defun sql-insert-all-values (conn)
- "SQL Databases: inserts all values for all files"
+ "SQL Databases: inserts all values for all files"
(dolist (file *umls-files*)
(sql-insert-values conn file)))
"SQL Databases: create all indexes"
(dolist (idx indexes)
(ignore-errors (sql-execute (drop-index-cmd (car idx) (cadr idx)) conn))
- (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
+ (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
(defun make-usrl (conn)
(if (eql :mysql *umls-sql-type*)
(sql-execute "create table USRL (sab varchar(80), srl integer)" 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)"
+ (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
(car tuple) (ensure-integer (cadr tuple)))
conn)))
(sql-create-indexes conn +custom-index-cols+)
(sql-create-special-tables conn)))
-(defun create-umls-db (&key (extension ".trans") (skip-translation nil))
- "SQL Databases: initializes entire database via SQL copy commands.
+(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."
(ensure-ucols+ufiles)
(ensure-preparse)
(sql-create-indexes conn +custom-index-cols+)
(sql-create-special-tables conn))))
-(defun translate-all-files (&optional (extension ".trans"))
+(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.RRF" *umls-files* :test #'string= :key #'fil))
(translate-files (find-ufile "MRXW_NONENG.RRF")
extension (noneng-lang-index-files)))
+(defun verify-translation-file (output-path input-ufiles)
+ "Returns t if translation file exists and is correct size. Warns and deletes incomplete translation file."
+ (when (probe-file output-path)
+ (let ((translated-lines 0)
+ (input-lines 0)
+ (eof (cons nil nil)))
+ (catch 'done-counting
+ (with-open-file (ts output-path :direction :input
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (do ()
+ ((eq (read-line ts nil eof) eof))
+ (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)))))
+ (cond
+ ((eql input-lines 0)
+ (error "Input lines is 0")
+ nil)
+ ((< 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)
+ t)
+ ((> translated-lines input-lines)
+ (error "Shouldn't happen. Translated lines of ~A is ~D, greater than input lines ~D"
+ output-path translated-lines input-lines)
+ (delete-file output-path)
+ nil)))))
+
(defun translate-files (out-ufile extension input-ufiles)
"Translate a umls file into a format suitable for sql copy cmd"
(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-ufile (line input-ufile)
- (translate-line out-ufile line ostream)
- (princ #\newline ostream)))))))
+ (when (verify-translation-file output-path input-ufiles)
+ (return-from translate-files output-path))
+ (with-open-file (ostream output-path :direction :output
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (dolist (input-ufile input-ufiles)
+ (with-umls-ufile (line input-ufile)
+ (translate-line out-ufile line ostream)
+ (princ #\newline ostream))))))
(defun translate-line (file line strm)
"Translate a single line for sql output"
(write-to-string ui)))
(escape-backslashes value))))
(print-separated-strings
- strm "|"
+ strm "|"
(mapcar #'col-value (remove-custom-cols (ucols file)) line)
(custom-col-values (custom-ucols-for-file file) line nil))))
(defun pg-copy-cmd (file extension)
- "Return postgresql copy statement for a file"
+ "Return postgresql copy statement for a file"
(format
nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
(table file) (ufile-pathname file extension)))
-(defun mysql-copy-cmd (file extension &key local-file)
- "Return mysql copy statement for a file"
+(defun mysql-copy-cmd (file extension &key (local-file t))
+ "Return mysql copy statement for a file"
(format
nil
"LOAD DATA ~AINFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
(if local-file "LOCAL " "")
- (ufile-pathname file extension) (table file)))
+ (namestring (ufile-pathname file extension)) (table file)))
+
-
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Routines for analyzing cost of fixed size storage
projects / umlisp.git / blobdiff