(format nil " (~d)" length)
"")))
((:postgresql :postgresql-socket)
- ;; FIXME: incorrect syntax
+ ;; FIXME: incorrect syntax for postgresql?
(if (integerp length)
(format nil "substr((~A)::text,1,~D)" colname length)
colname))
(sql-create-indexes conn +custom-index-cols+)
(sql-create-special-tables conn)))
-(defun create-umls-db (&key (extension "-trans") (skip-translation nil))
+(defun create-umls-db (&key (extension "-trans") (skip-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
+ (when verbose (format t "UMLS Import: Converting text UMLS files to optimized format.~%"))
(translate-all-files extension))
(let ((copy-cmd
(ecase (umls-sql-type)
(sql-drop-tables conn)
(sql-create-tables conn)
(dolist (file *umls-files*)
+ (when verbose (format t "UMLS Import: Importing file ~A.~%" file))
(sql-execute (funcall copy-cmd file extension) conn))
+ (When verbose (format t "UMLS Import: Creating SQL indices.~%"))
(sql-create-indexes conn)
+ (When verbose (format t "UMLS Import: Creating custom tables.~%"))
(sql-create-custom-tables conn)
+ (When verbose (format t "UMLS Import: Creating custom indices.~%"))
(sql-create-indexes conn +custom-index-cols+)
- (sql-create-special-tables conn))))
+ (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"
(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)))))
+ (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)
((eql input-lines translated-lines)
(format t "Translated file ~A already exists: skipping...~%" output-path)
t)
+ ((eql input-lines 0)
+ (warn "The number of input lines is 0 for output file ~A." 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)