(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))
(: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)))
(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))
"SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
(ensure-ucols+ufiles)
(sql-create-indexes conn)
(sql-create-custom-tables conn)
(sql-create-indexes conn +custom-index-cols+)
- (sql-create-special-tables conn))))
+ (sql-create-special-tables conn)))
+ t)
-(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))
(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)
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)
+(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)))
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