(ignore-errors (sql-execute (drop-index-cmd (car idx) (cadr idx)) conn))
(sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn)))
(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-insert-all-values conn)
(sql-create-indexes conn)
(sql-create-custom-tables conn)
(sql-insert-all-values conn)
(sql-create-indexes conn)
(sql-create-custom-tables conn)
"SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
"SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
- (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)
- (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-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.~%"))
-(defun translate-all-files (&optional (extension "-trans"))
- "Copy translated files and return postgresql copy commands to import"
- (make-noneng-index-file extension)
+(defun translate-all-files (&key (extension "-trans") verbose force)
+ "Translate all *umls-files* to optimized import format."
+ (when verbose (format t "UMLS Import: Translating file ~A.~%" (fil (find-ufile "MRXW_NONENG.RRF"))))
+ (make-noneng-index-file extension :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."
(defun verify-translation-file (output-path input-ufiles)
"Returns t if translation file exists and is correct size. Warns and deletes incomplete translation file."
(incf translated-lines)))
(dolist (input-ufile input-ufiles)
(with-umls-ufile (line input-ufile)
(incf translated-lines)))
(dolist (input-ufile input-ufiles)
(with-umls-ufile (line input-ufile)
((< input-lines translated-lines)
(format t "Translated file ~A incomplete, deleting...~%" output-path)
(delete-file output-path)
((< input-lines translated-lines)
(format t "Translated file ~A incomplete, deleting...~%" output-path)
(delete-file output-path)
((eql input-lines translated-lines)
(format t "Translated file ~A already exists: skipping...~%" output-path)
t)
((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)))))
((> 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)))))
"Translate a umls file into a format suitable for sql copy cmd"
(let ((output-path (ufile-pathname out-ufile extension)))
"Translate a umls file into a format suitable for sql copy cmd"
(let ((output-path (ufile-pathname out-ufile extension)))
#+(and clisp unicode) :external-format
#+(and clisp unicode) charset:utf-8)
(dolist (input-ufile input-ufiles)
#+(and clisp unicode) :external-format
#+(and clisp unicode) charset:utf-8)
(dolist (input-ufile input-ufiles)
- (incf row (1+ (cmax ucol))))
+ (let* ((col-max (cmax ucol))
+ (max-with-delim (1+ col-max)))
+ (declare (type (integer 0 1000000) col-max max-with-delim))
+ (incf row max-with-delim)))