(format nil "DROP INDEX ~a"
(concatenate 'string tablename "_" colname "_X")))))
-(defun sql-create-indexes (conn &optional (indexes +index-cols+))
+(defun sql-create-indexes (conn &key (indexes +index-cols+) verbose)
"SQL Databases: create all indexes"
(dolist (idx indexes)
+ (when verbose (format t "UMLS Import: Creating index ~S.~%" idx))
(ignore-errors (sql-execute (drop-index-cmd (car idx) (cadr idx)) conn))
(sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
(make-usrl conn)
(make-ustats))
-(defun create-umls-db-by-insert ()
+(defun create-umls-db-by-insert (&key verbose)
"SQL Databases: initializes entire database via SQL insert commands"
(ensure-ucols+ufiles)
(ensure-preparse)
(sql-insert-all-values conn)
(sql-create-indexes conn)
(sql-create-custom-tables conn)
- (sql-create-indexes conn +custom-index-cols+)
+ (sql-create-indexes conn :indexes +custom-index-cols+ :verbose verbose)
(sql-create-special-tables conn)))
-(defun create-umls-db (&key (extension "-trans") (skip-translation nil))
+(defun create-umls-db (&key (extension "-trans") (force-translation nil) (verbose nil))
"SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
+ (when verbose (format t "UMLS Import: Starting.~%"))
(ensure-ucols+ufiles)
+ (when verbose (format t "UMLS Import: Preparsing files.~%"))
(ensure-preparse)
- (unless skip-translation
- (translate-all-files extension))
+ (when verbose (format t "UMLS Import: Converting text UMLS files to optimized format.~%"))
+ (translate-all-files :extension extension :verbose verbose :force force-translation)
(let ((copy-cmd
(ecase (umls-sql-type)
(:mysql #'mysql-copy-cmd)
(sql-drop-tables conn)
(sql-create-tables conn)
(dolist (file *umls-files*)
+ (when verbose (format t "UMLS Import: Importing file ~A to SQL.~%" (fil file)))
(sql-execute (funcall copy-cmd file extension) conn))
- (sql-create-indexes conn)
+ (When verbose (format t "UMLS Import: Creating SQL indices.~%"))
+ (sql-create-indexes conn :verbose verbose)
+ (When verbose (format t "UMLS Import: Creating custom tables.~%"))
(sql-create-custom-tables conn)
- (sql-create-indexes conn +custom-index-cols+)
+ (When verbose (format t "UMLS Import: Creating custom indices.~%"))
+ (sql-create-indexes conn :indexes +custom-index-cols+ :verbose verbose)
+ (When verbose (format t "UMLS Import: Creating special tables.~%"))
(sql-create-special-tables conn)))
+ (When verbose (format t "UMLS Import: Completed.~%"))
t)
-(defun translate-all-files (&optional (extension "-trans"))
- "Copy translated files and return postgresql copy commands to import"
+(defun translate-all-files (&key (extension "-trans") verbose force)
+ "Translate all *umls-files* to optimized import format."
(make-noneng-index-file extension)
(dolist (f (remove "MRXW_NONENG.RRF" *umls-files* :test #'string= :key #'fil))
- (translate-umls-file f extension)))
+ (when verbose (format t "UMLS Import: translating file ~S.~%" (fil f)))
+ (translate-umls-file f extension :force force)))
-(defun translate-umls-file (file extension)
+(defun translate-umls-file (file extension &key force)
"Translate a umls file into a format suitable for sql copy cmd"
- (translate-files file extension (list file)))
+ (translate-files file extension (list file) :force force))
-(defun make-noneng-index-file (extension)
+(defun make-noneng-index-file (extension &key force)
"Make non-english index file"
(translate-files (find-ufile "MRXW_NONENG.RRF")
- extension (noneng-lang-index-files)))
+ extension (noneng-lang-index-files) :force force))
(defun verify-translation-file (output-path input-ufiles)
"Returns t if translation file exists and is correct size. Warns and deletes incomplete translation file."
(delete-file output-path)
nil)))))
-(defun translate-files (out-ufile extension input-ufiles)
+(defun translate-files (out-ufile extension input-ufiles &key force)
"Translate a umls file into a format suitable for sql copy cmd"
(let ((output-path (ufile-pathname out-ufile extension)))
- (when (verify-translation-file output-path input-ufiles)
+ (when (and (not force) (verify-translation-file output-path input-ufiles))
(return-from translate-files output-path))
(with-open-file (ostream output-path :direction :output
+ :if-exists :overwrite
#+(and clisp unicode) :external-format
#+(and clisp unicode) charset:utf-8)
(dolist (input-ufile input-ufiles)