(defun create-table-cmd (file)
"Return sql command to create a table"
- (let ((col-func
- (lambda (c)
- (let ((sqltype (sqltype c)))
- (concatenate 'string
- (col c)
- " "
- (if (or (string-equal sqltype "VARCHAR")
- (string-equal sqltype "CHAR"))
- (format nil "~a (~a)" sqltype (cmax c))
- sqltype))))))
+ (let ((col-func
+ (lambda (c)
+ (let ((sqltype (sqltype c)))
+ (concatenate 'string
+ (col c)
+ " "
+ (if (or (string-equal sqltype "VARCHAR")
+ (string-equal sqltype "CHAR"))
+ (format nil "~a (~a)" sqltype (cmax c))
+ sqltype))))))
(format nil "CREATE TABLE ~a (~{~a~^,~})" (table file)
- (mapcar col-func (ucols file)))))
+ (mapcar col-func (ucols file)))))
(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)
- (insert-col-value col value)
- (quote-str col)))))
+ (lambda (col value)
+ (concatenate 'string (quote-str col)
+ (insert-col-value col value)
+ (quote-str col)))))
(format
nil "INSERT INTO ~a (~{~a~^,~}) VALUES (~A)"
(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 custom-col-value (col values doquote)
(let ((custom-value (funcall (custom-value-fun col) values)))
(if custom-value
- (if doquote
- (concatenate 'string (quote-str col)
- (escape-backslashes custom-value)
- (quote-str col))
- (escape-backslashes custom-value))
- "")))
+ (if doquote
+ (concatenate 'string (quote-str col)
+ (escape-backslashes custom-value)
+ (quote-str col))
+ (escape-backslashes custom-value))
+ "")))
(defun custom-col-values (ucols values doquote)
"Returns a list of string column values for SQL inserts for custom columns"
(defun find-custom-col (filename col)
(find-if (lambda (x) (and (string-equal filename (car x))
- (string-equal col (cadr x)))) +custom-cols+))
+ (string-equal col (cadr x)))) +custom-cols+))
(defun custom-colnames-for-filename (filename)
(mapcar #'cadr (find-custom-cols-for-filename filename)))
(defun noneng-lang-index-files ()
(remove-if-not
(lambda (f) (and (> (length (fil f)) 4)
- (string-equal (fil f) "MRXW." :end1 5)
- (not (string-equal (fil f) "MRXW.ENG"))
- (not (string-equal (fil f) "MRXW.NONENG"))))
+ (string-equal (fil f) "MRXW." :end1 5)
+ (not (string-equal (fil f) "MRXW.ENG"))
+ (not (string-equal (fil f) "MRXW.NONENG"))))
*umls-files*))
;;; SQL Command Functions
(defun create-index-cmd (colname tablename length)
"Return sql create index command"
(format nil "CREATE INDEX ~a ON ~a (~a)"
- (concatenate 'string tablename "_" colname "_X")
- tablename
- (case *umls-sql-type*
- (:mysql
- (concatenate 'string colname
- (if (integerp length)
- (format nil " (~d)" length)
- "")))
- ((:postgresql :postgresql-socket)
- ;; FIXME: incorrect syntax
- (if (integerp length)
- (format nil "substr((~A)::text,1,~D)" colname length)
- colname))
- (t
- colname))))
+ (concatenate 'string tablename "_" colname "_X")
+ tablename
+ (case *umls-sql-type*
+ (:mysql
+ (concatenate 'string colname
+ (if (integerp length)
+ (format nil " (~d)" length)
+ "")))
+ ((:postgresql :postgresql-socket)
+ ;; FIXME: incorrect syntax
+ (if (integerp length)
+ (format nil "substr((~A)::text,1,~D)" colname length)
+ colname))
+ (t
+ colname))))
(defun create-all-tables-cmdfile ()
"Return sql commands to create all tables. Not need for automated SQL import"
(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)))
"SQL Databases: create all custom tables"
(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)))
(case *umls-sql-type*
(:mysql
(format nil "DROP INDEX ~a ON ~a"
- (concatenate 'string tablename "_" colname "_X")
- tablename))
+ (concatenate 'string tablename "_" colname "_X")
+ tablename))
(t
(format nil "DROP INDEX ~a"
- (concatenate 'string tablename "_" colname "_X")))))
+ (concatenate 'string tablename "_" colname "_X")))))
(defun sql-create-indexes (conn &optional (indexes +index-cols+))
"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*)
(ignore-errors (sql-execute "drop table USRL" conn)))
(sql-execute "create table USRL (sab varchar(80), srl integer)" conn)
(dolist (tuple (mutex-sql-query
- "select distinct SAB,SRL from MRSO order by SAB asc"))
- (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
- (car tuple) (ensure-integer (cadr tuple)))
- conn)))
+ "select distinct SAB,SRL from MRSO order by SAB asc"))
+ (sql-execute (format nil "insert into USRL (sab,srl) values ('~a',~d)"
+ (car tuple) (ensure-integer (cadr tuple)))
+ conn)))
(defun sql-create-special-tables (conn)
(make-usrl conn)
(sql-create-special-tables conn)))
(defun create-umls-db (&key (extension ".trans") (skip-translation nil))
- "SQL Databases: initializes entire database via SQL copy commands.
+ "SQL Databases: initializes entire database via SQL copy commands.
This is much faster that using create-umls-db-insert."
(ensure-ucols+ufiles)
(ensure-preparse)
(unless skip-translation
(translate-all-files extension))
(let ((copy-cmd
- (ecase (umls-sql-type)
- (:mysql #'mysql-copy-cmd)
- (:postgresql #'pg-copy-cmd))))
+ (ecase (umls-sql-type)
+ (:mysql #'mysql-copy-cmd)
+ (:postgresql #'pg-copy-cmd))))
(with-sql-connection (conn)
(clsql:truncate-database :database conn)
(sql-drop-tables conn)
(sql-create-tables conn)
(dolist (file *umls-files*)
- (sql-execute (funcall copy-cmd file extension) conn))
+ (sql-execute (funcall copy-cmd file extension) conn))
(sql-create-indexes conn)
(sql-create-custom-tables conn)
(sql-create-indexes conn +custom-index-cols+)
(defun make-noneng-index-file (extension)
"Make non-english index file"
(translate-files (find-ufile "MRXW.NONENG")
- extension (noneng-lang-index-files)))
+ extension (noneng-lang-index-files)))
(defun translate-files (out-ufile extension input-ufiles)
"Translate a umls file into a format suitable for sql copy cmd"
(let ((output-path (umls-pathname (fil out-ufile) extension)))
(if (probe-file output-path)
- (format t "File ~A already exists: skipping~%" 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-file (line (fil input-ufile))
- (translate-line out-ufile line ostream)
- (princ #\newline ostream)))))))
+ (dolist (input-ufile input-ufiles)
+ (with-umls-file (line (fil input-ufile))
+ (translate-line out-ufile line ostream)
+ (princ #\newline ostream)))))))
(defun translate-line (file line strm)
"Translate a single line for sql output"
(flet ((col-value (col value)
- (if (eq (datatype col) 'sql-u)
- (let ((ui (parse-ui value "")))
- (if (stringp ui)
- ui
- (write-to-string ui)))
- (escape-backslashes value))))
+ (if (eq (datatype col) 'sql-u)
+ (let ((ui (parse-ui value "")))
+ (if (stringp ui)
+ ui
+ (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) (umls-pathname (fil file) extension)))
(defun mysql-copy-cmd (file extension &key local-file)
- "Return mysql copy statement for a file"
+ "Return mysql copy statement for a file"
(format
nil
"LOAD DATA ~AINFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
(if local-file "LOCAL " "")
(umls-pathname (fil file) extension) (table file)))
-
+
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Routines for analyzing cost of fixed size storage
(defun umls-fixed-size-waste ()
"Display storage waste if using all fixed size storage"
(let ((totalwaste 0)
- (totalunavoidable 0)
- (totalavoidable 0)
- (unavoidable '())
- (avoidable '()))
+ (totalunavoidable 0)
+ (totalavoidable 0)
+ (unavoidable '())
+ (avoidable '()))
(dolist (file *umls-files*)
(dolist (col (ucols file))
- (let* ((avwaste (- (cmax col) (av col)))
- (cwaste (* avwaste (rws file))))
- (when (plusp cwaste)
- (if (<= avwaste 6)
- (progn
- (incf totalunavoidable cwaste)
- (push (list (fil file) (col col)
- avwaste cwaste)
- unavoidable))
- (progn
- (incf totalavoidable cwaste)
- (push (list (fil file) (col col)
- avwaste cwaste)
- avoidable)))
- (incf totalwaste cwaste)))))
+ (let* ((avwaste (- (cmax col) (av col)))
+ (cwaste (* avwaste (rws file))))
+ (when (plusp cwaste)
+ (if (<= avwaste 6)
+ (progn
+ (incf totalunavoidable cwaste)
+ (push (list (fil file) (col col)
+ avwaste cwaste)
+ unavoidable))
+ (progn
+ (incf totalavoidable cwaste)
+ (push (list (fil file) (col col)
+ avwaste cwaste)
+ avoidable)))
+ (incf totalwaste cwaste)))))
(values totalwaste totalavoidable totalunavoidable
- (nreverse avoidable) (nreverse unavoidable))))
+ (nreverse avoidable) (nreverse unavoidable))))
(defun display-waste ()
(ensure-ucols+ufiles)
(declare (fixnum max))
(dolist (ucol *umls-cols*)
(when (> (cmax ucol) max)
- (setq max (cmax ucol))))
+ (setq max (cmax ucol))))
max))
(defun max-umls-row ()
(let ((rowsizes '()))
(dolist (file *umls-files*)
(let ((row 0))
- (dolist (ucol (ucols file))
- (incf row (1+ (cmax ucol))))
- (push row rowsizes)))
+ (dolist (ucol (ucols file))
+ (incf row (1+ (cmax ucol))))
+ (push row rowsizes)))
(car (sort rowsizes #'>))))
projects / umlisp-orf.git / blobdiff