--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: sql-create
+;;;; Purpose: Create SQL database for UMLisp
+;;;; Author: Kevin M. Rosenberg
+;;;; Created: Apr 2000
+;;;;
+;;;; $Id$
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2004 by Kevin M. Rosenberg, M.D.
+;;;;
+;;;; UMLisp users are granted the rights to distribute and use this software
+;;;; as governed by the terms of the GNU General Public License.
+;;;; *************************************************************************
+
+(in-package #:umlisp-orf)
+
+(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))))))
+ (format nil "CREATE TABLE ~a (~{~a~^,~})" (table 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))
+ value
+ (format nil "~A" (funcall (parse-fun col) value))))
+
+(defun insert-values-cmd (file 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)))))
+ (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))
+ "")))
+
+(defun custom-col-values (ucols values doquote)
+ "Returns a list of string column values for SQL inserts for custom columns"
+ (loop for col in ucols collect (custom-col-value col values doquote)))
+
+(defun remove-custom-cols (cols)
+ "Remove custom cols from a list col umls-cols"
+ (remove-if #'custom-value-fun cols))
+
+(defun find-custom-cols-for-filename (filename)
+ (remove-if-not (lambda (x) (string-equal filename (car x))) +custom-cols+))
+
+(defun find-custom-col (filename col)
+ (find-if (lambda (x) (and (string-equal filename (car x))
+ (string-equal col (cadr x)))) +custom-cols+))
+
+(defun custom-colnames-for-filename (filename)
+ (mapcar #'cadr (find-custom-cols-for-filename filename)))
+
+(defun custom-ucols-for-file (file)
+ (remove-if-not #'custom-value-fun (ucols file)))
+
+(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"))))
+ *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))))
+
+(defun create-all-tables-cmdfile ()
+ "Return sql commands to create all tables. Not need for automated SQL import"
+ (mapcar (lambda (f) (format nil "~a~%~%" (create-table-cmd f))) *umls-files*))
+
+;; SQL Execution functions
+
+(defun sql-drop-tables (conn)
+ "SQL Databases: drop all tables"
+ (dolist (file *umls-files*)
+ (ignore-errors
+ (sql-execute (format nil "DROP TABLE ~a" (table file)) conn))))
+
+(defun sql-create-tables (conn)
+ "SQL Databases: create all tables"
+ (dolist (file *umls-files*)
+ (sql-execute (create-table-cmd file) conn)))
+
+(defun sql-create-custom-tables (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"
+ (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"
+ (dolist (file *umls-files*)
+ (sql-insert-values conn file)))
+
+(defun drop-index-cmd (colname tablename)
+ "Return sql create index command"
+ (case *umls-sql-type*
+ (:mysql
+ (format nil "DROP INDEX ~a ON ~a"
+ (concatenate 'string tablename "_" colname "_X")
+ tablename))
+ (t
+ (format nil "DROP INDEX ~a"
+ (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)))
+
+(defun make-usrl (conn)
+ (if (eql :mysql *umls-sql-type*)
+ (sql-execute "drop table if exists USRL" conn)
+ (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)))
+
+(defun sql-create-special-tables (conn)
+ (make-usrl conn)
+ (make-ustats))
+
+(defun create-umls-db-by-insert ()
+ "SQL Databases: initializes entire database via SQL insert commands"
+ (ensure-ucols+ufiles)
+ (ensure-preparse)
+ (with-sql-connection (conn)
+ (sql-drop-tables conn)
+ (sql-create-tables conn)
+ (sql-insert-all-values conn)
+ (sql-create-indexes conn)
+ (sql-create-custom-tables conn)
+ (sql-create-indexes conn +custom-index-cols+)
+ (sql-create-special-tables conn)))
+
+(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)
+ (ensure-preparse)
+ (unless skip-translation
+ (translate-all-files extension))
+ (let ((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-create-indexes conn)
+ (sql-create-custom-tables conn)
+ (sql-create-indexes conn +custom-index-cols+)
+ (sql-create-special-tables conn))))
+
+(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" *umls-files* :test #'string= :key #'fil))
+ (translate-umls-file f extension)))
+
+(defun translate-umls-file (file extension)
+ "Translate a umls file into a format suitable for sql copy cmd"
+ (translate-files file extension (list file)))
+
+(defun make-noneng-index-file (extension)
+ "Make non-english index file"
+ (translate-files (find-ufile "MRXW.NONENG")
+ 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)
+ (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)))))))
+
+(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))))
+ (print-separated-strings
+ 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"
+ (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"
+ (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 '()))
+ (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)))))
+ (values totalwaste totalavoidable totalunavoidable
+ (nreverse avoidable) (nreverse unavoidable))))
+
+(defun display-waste ()
+ (ensure-ucols+ufiles)
+ (multiple-value-bind (tw ta tu al ul) (umls-fixed-size-waste)
+ (format t "Total waste: ~d~%" tw)
+ (format t "Total avoidable: ~d~%" ta)
+ (format t "Total unavoidable: ~d~%" tu)
+ (format t "Avoidable:~%")
+ (dolist (w al)
+ (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
+ (format t "Unavoidable:~%")
+ (dolist (w ul)
+ (format t " (~a,~a): ~a,~a~%" (car w) (cadr w) (caddr w) (cadddr w)))
+ ))
+
+(defun max-umls-field ()
+ "Return length of longest field"
+ (declare (optimize (speed 3) (space 0)))
+ (ensure-ucols+ufiles)
+ (let ((max 0))
+ (declare (fixnum max))
+ (dolist (ucol *umls-cols*)
+ (when (> (cmax ucol) max)
+ (setq max (cmax ucol))))
+ max))
+
+(defun max-umls-row ()
+ "Return length of longest row"
+ (declare (optimize (speed 3) (space 0)))
+ (ensure-ucols+ufiles)
+ (let ((rowsizes '()))
+ (dolist (file *umls-files*)
+ (let ((row 0))
+ (dolist (ucol (ucols file))
+ (incf row (1+ (cmax ucol))))
+ (push row rowsizes)))
+ (car (sort rowsizes #'>))))
projects / umlisp-orf.git / blobdiff