;;;; Programmer: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-common.lisp,v 1.2 2002/10/09 23:03:41 kevin Exp $
+;;;; $Id: parse-common.lisp,v 1.3 2002/10/18 03:57:39 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
(umls-file-fields file))))
-;; SQL command functions
-
-(defun create-table-cmd (file)
-"Return sql command to create a table"
- (let ((col-func
- (lambda (c)
- (let ((sqltype (umls-col-sqltype c)))
- (concatenate 'string (umls-col-col c)
- " "
- (if (or (string-equal sqltype "VARCHAR")
- (string-equal sqltype "CHAR"))
- (format nil "~a (~a)" sqltype (umls-col-max c))
- sqltype)
- ",")))))
- (format nil "CREATE TABLE ~a (~a)" (umls-file-table file)
- (string-trim-last-character
- (mapcar-append-string col-func (umls-cols-for-umls-file 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-values-cmd (file values)
-"Return sql insert command for a row of values"
- (let ((insert-func
- (lambda (col value)
- (concatenate
- 'string
- (umls-col-quotechar col)
- (if (null (umls-col-parsefunc col))
- value
- (format nil "~A" (funcall (umls-col-parsefunc col) value)))
- (umls-col-quotechar col)
- ","))))
- (format
- nil "INSERT INTO ~a (~a) VALUES (~a)"
- (umls-file-table file)
- (string-trim-last-character
- (mapcar-append-string (lambda (c) (concatenate 'string c ","))
- (umls-file-fields file)))
- (string-trim-last-character
- (concatenate 'string
- (mapcar2-append-string insert-func
- (remove-custom-cols (umls-file-colstructs file))
- values)
- (custom-col-values (custom-colstructs-for-file file) values "," t)))
- )))
-
-(defun custom-col-values (colstructs values delim doquote)
- "Returns string of column values for SQL inserts for custom columns"
- (let ((result ""))
- (dolist (col colstructs)
- (let* ((func (umls-col-custom-value-func col))
- (custom-value (funcall func values)))
- (string-append result
- (if doquote (umls-col-quotechar col))
- (escape-backslashes custom-value)
- (if doquote (umls-col-quotechar col))
- delim)))
- result))
-
-(defun remove-custom-cols (cols)
- "Remove custom cols from a list col umls-cols"
- (remove-if #'umls-col-custom-value-func 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-colstructs-for-file (file)
- (remove-if-not #'umls-col-custom-value-func (umls-file-colstructs file)))
-
-(defun noneng-lang-index-files ()
- (remove-if-not (lambda (f) (and (> (length (umls-file-fil f)) 4)
- (string-equal (umls-file-fil f) "MRXW." :end1 5)
- (not (string-equal (umls-file-fil f) "MRXW.ENG"))
- (not (string-equal (umls-file-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 ~a)"
- (concatenate 'string tablename "_" colname "_X") tablename colname
- (if (integerp length)
- (format nil "(~d)" length)
- "")))
-
-(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"
- (mapcar
- (lambda (file)
- (ignore-errors
- (sql-execute (format nil "DROP TABLE ~a" (umls-file-table file)) conn)))
- *umls-files*))
-
-(defun sql-create-tables (conn)
-"SQL Databases: create all tables"
- (mapcar (lambda (file) (sql-execute (create-table-cmd file) conn)) *umls-files*))
-
-(defun sql-create-custom-tables (conn)
-"SQL Databases: create all custom tables"
- (mapcar (lambda (ct)
- (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn))
- +custom-tables+))
-
-(defun sql-insert-values (conn file)
-"SQL Databases: inserts all values for a file"
- (with-umls-file (line (umls-file-fil file))
- (sql-execute (insert-values-cmd file line) conn)))
-
-(defun sql-insert-all-values (conn)
-"SQL Databases: inserts all values for all files"
- (mapcar (lambda (file) (sql-insert-values conn file)) *umls-files*))
-
-(defun sql-create-indexes (conn &optional (indexes +index-cols+))
-"SQL Databases: create all indexes"
-(mapcar
- (lambda (idx)
- (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn))
- indexes))
-
-(defun create-umls-db-by-insert ()
-"SQL Databases: initializes entire database via SQL insert commands"
- (init-umls)
- (init-hash-table)
- (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+)))
-
-(defun create-umls-db (&optional (extension ".trans")
- (copy-cmd #'mysql-copy-cmd))
- "SQL Databases: initializes entire database via SQL copy commands"
- (init-umls)
- (init-hash-table)
- (translate-all-files extension)
- (with-sql-connection (conn)
- (sql-drop-tables conn)
- (sql-create-tables conn)
- (mapcar
- #'(lambda (file) (sql-execute (funcall copy-cmd file extension) conn))
- *umls-files*)
- (sql-create-indexes conn)
- (sql-create-custom-tables conn)
- (sql-create-indexes conn +custom-index-cols+)))
-
-(defun translate-all-files (&optional (extension ".trans"))
-"Copy translated files and return postgresql copy commands to import"
- (make-noneng-index-file extension)
- (mapcar (lambda (f) (translate-file f extension)) *umls-files*))
-
-(defun translate-file (file extension)
- "Translate a umls file into a format suitable for sql copy cmd"
- (let ((path (umls-pathname (umls-file-fil file) extension)))
- (if (probe-file path)
- (progn
- (format t "File ~A already exists: skipping~%" path)
- nil)
- (with-open-file (ostream path :direction :output)
- (with-umls-file (line (umls-file-fil file))
- (princ (umls-translate file line) ostream)
- (princ #\newline ostream))
- t))))
-
-(defun make-noneng-index-file (extension)
- "Make non-english index file"
- (let* ((outfile (find-umls-file "MRXW.NONENG"))
- (path (umls-pathname (umls-file-fil outfile) extension)))
-
- (if (probe-file path)
- (progn
- (format t "File ~A already exists: skipping~%" path)
- nil)
- (progn
- (with-open-file (ostream path :direction :output)
- (dolist (inputfile (noneng-lang-index-files))
- (with-umls-file (line (umls-file-fil inputfile))
- (princ (umls-translate outfile line) ostream) ;; use outfile for custom cols
- (princ #\newline ostream))))
- t))))
-
-(defun pg-copy-cmd (file extension)
-"Return postgresql copy statement for a file"
- (format nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
- (umls-file-table file) (umls-pathname (umls-file-fil file) extension)))
-
-(defun mysql-copy-cmd (file extension)
-"Return mysql copy statement for a file"
- (format nil "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
- (umls-pathname (umls-file-fil file) extension) (umls-file-table file)))
-
-(defun umls-translate (file line)
-"Translate a single line for sql output"
-(string-trim-last-character
- (concatenate 'string
- (mapcar2-append-string
- (lambda (col value)
- (concatenate
- 'string
- (if (eq (umls-col-datatype col) 'sql-u)
- (format nil "~d" (parse-ui value ""))
- (escape-backslashes value))
- "|"))
- (remove-custom-cols (umls-file-colstructs file))
- line)
- (custom-col-values (custom-colstructs-for-file file) line "|" nil))))
-
+;;; Routines for analyzing cost of fixed size storage
(defun umls-fixed-size-waste ()
"Display storage waste if using all fixed size storage"
--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: sql-create
+;;;; Purpose: Create SQL database for UMLisp
+;;;; Programmer: Kevin M. Rosenberg
+;;;; Date Started: Apr 2000
+;;;;
+;;;; $Id: sql-create.lisp,v 1.1 2002/10/18 03:57:39 kevin Exp $
+;;;;
+;;;; This file, part of UMLisp, is
+;;;; Copyright (c) 2000-2002 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)
+(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))
+
+
+(defun create-table-cmd (file)
+"Return sql command to create a table"
+ (let ((col-func
+ (lambda (c)
+ (let ((sqltype (umls-col-sqltype c)))
+ (concatenate 'string (umls-col-col c)
+ " "
+ (if (or (string-equal sqltype "VARCHAR")
+ (string-equal sqltype "CHAR"))
+ (format nil "~a (~a)" sqltype (umls-col-max c))
+ sqltype)
+ ",")))))
+ (format nil "CREATE TABLE ~a (~a)" (umls-file-table file)
+ (string-trim-last-character
+ (mapcar-append-string col-func (umls-cols-for-umls-file 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-values-cmd (file values)
+"Return sql insert command for a row of values"
+ (let ((insert-func
+ (lambda (col value)
+ (concatenate
+ 'string
+ (umls-col-quotechar col)
+ (if (null (umls-col-parsefunc col))
+ value
+ (format nil "~A" (funcall (umls-col-parsefunc col) value)))
+ (umls-col-quotechar col)
+ ","))))
+ (format
+ nil "INSERT INTO ~a (~a) VALUES (~a)"
+ (umls-file-table file)
+ (string-trim-last-character
+ (mapcar-append-string (lambda (c) (concatenate 'string c ","))
+ (umls-file-fields file)))
+ (string-trim-last-character
+ (concatenate 'string
+ (mapcar2-append-string insert-func
+ (remove-custom-cols (umls-file-colstructs file))
+ values)
+ (custom-col-values (custom-colstructs-for-file file) values "," t)))
+ )))
+
+(defun custom-col-values (colstructs values delim doquote)
+ "Returns string of column values for SQL inserts for custom columns"
+ (let ((result ""))
+ (dolist (col colstructs)
+ (let* ((func (umls-col-custom-value-func col))
+ (custom-value (funcall func values)))
+ (string-append result
+ (if doquote (umls-col-quotechar col))
+ (escape-backslashes custom-value)
+ (if doquote (umls-col-quotechar col))
+ delim)))
+ result))
+
+(defun remove-custom-cols (cols)
+ "Remove custom cols from a list col umls-cols"
+ (remove-if #'umls-col-custom-value-func 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-colstructs-for-file (file)
+ (remove-if-not #'umls-col-custom-value-func (umls-file-colstructs file)))
+
+(defun noneng-lang-index-files ()
+ (remove-if-not (lambda (f) (and (> (length (umls-file-fil f)) 4)
+ (string-equal (umls-file-fil f) "MRXW." :end1 5)
+ (not (string-equal (umls-file-fil f) "MRXW.ENG"))
+ (not (string-equal (umls-file-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 ~a)"
+ (concatenate 'string tablename "_" colname "_X") tablename colname
+ (if (integerp length)
+ (format nil "(~d)" length)
+ "")))
+
+(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"
+ (mapcar
+ (lambda (file)
+ (ignore-errors
+ (sql-execute (format nil "DROP TABLE ~a" (umls-file-table file)) conn)))
+ *umls-files*))
+
+(defun sql-create-tables (conn)
+"SQL Databases: create all tables"
+ (mapcar (lambda (file) (sql-execute (create-table-cmd file) conn)) *umls-files*))
+
+(defun sql-create-custom-tables (conn)
+"SQL Databases: create all custom tables"
+ (mapcar (lambda (ct)
+ (sql-execute (create-custom-table-cmd (car ct) (cadr ct)) conn))
+ +custom-tables+))
+
+(defun sql-insert-values (conn file)
+"SQL Databases: inserts all values for a file"
+ (with-umls-file (line (umls-file-fil file))
+ (sql-execute (insert-values-cmd file line) conn)))
+
+(defun sql-insert-all-values (conn)
+"SQL Databases: inserts all values for all files"
+ (mapcar (lambda (file) (sql-insert-values conn file)) *umls-files*))
+
+(defun sql-create-indexes (conn &optional (indexes +index-cols+))
+"SQL Databases: create all indexes"
+(mapcar
+ (lambda (idx)
+ (sql-execute (create-index-cmd (car idx) (cadr idx) (caddr idx)) conn))
+ indexes))
+
+(defun make-usrl (conn)
+ (sql-execute "drop table if exists 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))
+
+(defun create-umls-db-by-insert ()
+"SQL Databases: initializes entire database via SQL insert commands"
+ (init-umls)
+ (init-hash-table)
+ (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)))
+
+(defun create-umls-db (&optional (extension ".trans")
+ (copy-cmd #'mysql-copy-cmd))
+ "SQL Databases: initializes entire database via SQL copy commands.
+This is much faster that using create-umls-db-insert."
+ (init-umls)
+ (init-hash-table)
+ (translate-all-files extension)
+ (with-sql-connection (conn)
+ (sql-drop-tables conn)
+ (sql-create-tables conn)
+ (mapcar
+ #'(lambda (file) (sql-execute (funcall copy-cmd file extension) conn))
+ *umls-files*)
+ (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)
+ (mapcar (lambda (f) (translate-file f extension)) *umls-files*))
+
+(defun translate-file (file extension)
+ "Translate a umls file into a format suitable for sql copy cmd"
+ (let ((path (umls-pathname (umls-file-fil file) extension)))
+ (if (probe-file path)
+ (progn
+ (format t "File ~A already exists: skipping~%" path)
+ nil)
+ (with-open-file (ostream path :direction :output)
+ (with-umls-file (line (umls-file-fil file))
+ (princ (umls-translate file line) ostream)
+ (princ #\newline ostream))
+ t))))
+
+(defun make-noneng-index-file (extension)
+ "Make non-english index file"
+ (let* ((outfile (find-umls-file "MRXW.NONENG"))
+ (path (umls-pathname (umls-file-fil outfile) extension)))
+
+ (if (probe-file path)
+ (progn
+ (format t "File ~A already exists: skipping~%" path)
+ nil)
+ (progn
+ (with-open-file (ostream path :direction :output)
+ (dolist (inputfile (noneng-lang-index-files))
+ (with-umls-file (line (umls-file-fil inputfile))
+ (princ (umls-translate outfile line) ostream) ;; use outfile for custom cols
+ (princ #\newline ostream))))
+ t))))
+
+(defun pg-copy-cmd (file extension)
+"Return postgresql copy statement for a file"
+ (format nil "COPY ~a FROM '~a' using delimiters '|' with null as ''"
+ (umls-file-table file) (umls-pathname (umls-file-fil file) extension)))
+
+(defun mysql-copy-cmd (file extension)
+"Return mysql copy statement for a file"
+ (format nil "LOAD DATA LOCAL INFILE \"~a\" INTO TABLE ~a FIELDS TERMINATED BY \"|\""
+ (umls-pathname (umls-file-fil file) extension) (umls-file-table file)))
+
+(defun umls-translate (file line)
+"Translate a single line for sql output"
+(string-trim-last-character
+ (concatenate 'string
+ (mapcar2-append-string
+ (lambda (col value)
+ (concatenate
+ 'string
+ (if (eq (umls-col-datatype col) 'sql-u)
+ (format nil "~d" (parse-ui value ""))
+ (escape-backslashes value))
+ "|"))
+ (remove-custom-cols (umls-file-colstructs file))
+ line)
+ (custom-col-values (custom-colstructs-for-file file) line "|" nil))))
+
+
+(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 (umls-file-colstructs file))
+ (let* ((avwaste (- (umls-col-max col) (umls-col-av col)))
+ (cwaste (* avwaste (umls-file-rws file))))
+ (unless (zerop cwaste)
+ (if (<= avwaste 6)
+ (progn
+ (incf totalunavoidable cwaste)
+ (setq unavoidable (append unavoidable (list (list (umls-file-fil file) (umls-col-col col) avwaste cwaste)))))
+ (progn
+ (incf totalavoidable cwaste)
+ (setq avoidable (append avoidable (list (list (umls-file-fil file) (umls-col-col col) avwaste cwaste))))))
+ (incf totalwaste cwaste)))))
+ (values totalwaste totalavoidable totalunavoidable avoidable unavoidable)))
+
+(defun display-waste ()
+ (unless *umls-files*
+ (init-umls))
+ (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"
+ (unless *umls-files*
+ (init-umls))
+ (let ((max 0))
+ (declare (fixnum max))
+ (dolist (col *umls-cols*)
+ (when (> (umls-col-max col) max)
+ (setq max (umls-col-max col))))
+ max))
+
+(defun max-umls-row ()
+ "Return length of longest row"
+ (if t
+ 6000 ;;; hack to use on systems without MRCOLS/MRFILES -- ok for UMLS2001
+ (progn
+ (unless *umls-files*
+ (init-umls))
+ (let ((rowsizes '()))
+ (dolist (file *umls-files*)
+ (let ((row 0)
+ (fields (umls-file-colstructs file)))
+ (dolist (field fields)
+ (incf row (1+ (umls-col-max field))))
+ (push row rowsizes)))
+ (car (sort rowsizes #'>))))))
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