X-Git-Url: http://git.kpe.io/?p=umlisp.git;a=blobdiff_plain;f=parse-common.lisp;h=b1395665b68eb612ef4de7fcfccaa16436ce2981;hp=07e5cc9a3138ee8f0a021af7b125efb63c988ef5;hb=HEAD;hpb=4e62898eedb688c0a44bd257cbcdee07f11ac058 diff --git a/parse-common.lisp b/parse-common.lisp index 07e5cc9..f7fab1e 100644 --- a/parse-common.lisp +++ b/parse-common.lisp @@ -2,15 +2,13 @@ ;;;; ************************************************************************* ;;;; FILE IDENTIFICATION ;;;; -;;;; Name: parse-common.lisp -;;;; Purpose: Common, stable parsing routines for UMLisp -;;;; Author: Kevin M. Rosenberg -;;;; Date Started: Apr 2000 -;;;; -;;;; $Id: parse-common.lisp,v 1.8 2003/05/06 07:44:07 kevin Exp $ +;;;; Name: parse-common.lisp +;;;; Purpose: Common, stable parsing routines for UMLisp +;;;; Author: Kevin M. Rosenberg +;;;; Created: Apr 2000 ;;;; ;;;; This file, part of UMLisp, is -;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D. +;;;; Copyright (c) 2000-2010 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. @@ -18,158 +16,379 @@ (in-package #:umlisp) -(eval-when (:compile-toplevel) - (declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3)))) +(defun ensure-ucols+ufiles (&optional (alwaysclear nil)) + "Initialize all UMLS file and column structures if not already initialized" + (handler-case + (when (or alwaysclear (null *umls-files*)) + (setf *umls-cols* nil *umls-files* nil) + (gen-ufiles) + (gen-ucols) + (set-ucols-for-ufiles *umls-files*) + (ensure-field-lengths)) + (error (e) + (warn "Error reading ucols+ufiles: ~A." e) + (setf *umls-cols* nil *umls-files* nil) + nil)) + t) + + +(defun add-ucols (ucols) + "Adds a ucol or list of ucols to *umls-cols*. Returns input value." + (setq *umls-cols* (append (mklist ucols) *umls-cols*)) + ucols) + +(defun add-ufiles (ufiles) + "Adds a ufile or list of ufiles to *umls-filess*. Returns input value." + (setq *umls-files* (append (mklist ufiles) *umls-files*)) + ufiles) + +(defun ufile-pathname (ufile &optional (extension "")) + "Return pathname for a umls filename with an optional extension" + (assert (typep ufile 'ufile)) + (let* ((dirs (nconc (list (dir ufile)) + (awhen (subdir ufile) (list it)))) + (name-list (delimited-string-to-list (fil ufile) #\.)) + (name (if (second name-list) + (first name-list) + (concatenate 'string (first name-list) (or extension "")))) + (type (when (second name-list) + (concatenate 'string (second name-list) (or extension ""))))) + (merge-pathnames + (make-pathname :name name :type type + :directory (cons :relative dirs)) + *umls-path*))) (defun umls-pathname (filename &optional (extension "")) -"Return pathname for a umls filename" +"Return pathname for a umls filename with an optional extension" (etypecase filename (string - (merge-pathnames - (make-pathname :name (concatenate 'string filename extension)) - (case (char filename 0) - ((#\M #\m) - *meta-path*) - ((#\L #\l) - *lex-path*) - ((#\S #\s) - *net-path*) - (t - *umls-path*)))) + (let* ((name-list (delimited-string-to-list filename #\.)) + (name (if (second name-list) + (first name-list) + (concatenate 'string (first name-list) (or extension "")))) + (type (when (second name-list) + (concatenate 'string (second name-list) (or extension ""))))) + (merge-pathnames + (make-pathname :name name :type type) + (case (schar filename 0) + ((#\M #\m) + *meta-path*) + ((#\L #\l) + *lex-path*) + ((#\S #\s) + *net-path*) + (t + *umls-path*))))) (pathname - filename))) + filename))) -(defun read-umls-line (strm &optional (eof 'eof)) - "Read a line from a UMLS stream, split into fields" - (let ((line (read-line strm nil eof))) - (if (eq line eof) - eof - (delimited-string-to-list line #\| t)))) ;;; Find field lengths for LEX and NET files -(defun file-field-lengths (files) - (let ((lengths '())) - (dolist (file files) - (setq file (fil file)) - (let (max-field count-field num-fields (count-lines 0)) - (with-umls-file (fields file) - (unless num-fields - (setq num-fields (length fields)) - (setq max-field (make-array num-fields :element-type 'fixnum - :initial-element 0)) - (setq count-field (make-array num-fields :element-type 'number - :initial-element 0))) - (dotimes (i (length fields)) - (declare (fixnum i)) - (let ((len (length (nth i fields)))) - (incf (aref count-field i) len) - (when (> len (aref max-field i)) - (setf (aref max-field i) len)))) - (incf count-lines)) - (dotimes (i num-fields) - (setf (aref count-field i) (float (/ (aref count-field i) count-lines)))) - (push (list file max-field count-field) lengths))) - (nreverse lengths))) - -(defun init-field-lengths () +(defun ensure-field-lengths () "Initial colstruct field lengths for files that don't have a measurement. Currently, these are the LEX and NET files." - (let ((measure-files '())) - (dolist (file *umls-files*) - (let ((filename (fil file))) - (unless (or (char= #\M (char filename 0)) - (char= #\m (char filename 0))) - (push file measure-files)))) - (let ((length-lists (file-field-lengths measure-files))) - (dolist (length-list length-lists) - (let* ((filename (car length-list)) - (max-field (cadr length-list)) - (av-field (caddr length-list)) - (file (find-ufile filename))) - (when file - (if (/= (length max-field) (length (fields file))) - (format t "Warning: Number of file fields ~A doesn't match length of fields in file structure ~S" - max-field file) - (dotimes (i (max (length max-field) (length (fields file)))) - (declare (fixnum i)) - (let* ((field (nth i (fields file))) - (col (find-ucol field filename))) - (if col - (progn - (setf (cmax col) (aref max-field i)) - (setf (av col) (aref av-field i)) - (add-datatype-to-col col (datatype-for-col (col col)))) - (error "can't find column ~A" field))))))))))) - + (dolist (length-list (ufiles-field-lengths (ufiles-to-measure))) + (destructuring-bind (filename fields-max fields-av count-lines) length-list + (let ((file (find-ufile filename))) + (unless file + (error "Can't find ~A filename in ufiles" filename)) + (if (zerop count-lines) + (warn "File ~A is empty." filename) + (progn + (unless (= (length fields-max) (length (fields file))) + (error + "Number of file fields ~A not equal to field count in ufile ~S" + fields-max file)) + (dotimes (i (length (fields file))) + (declare (fixnum i)) + (let* ((field (nth i (fields file))) + (col (find-ucol field filename))) + (unless col + (error "can't find column ~A" field)) + (setf (cmax col) (aref fields-max i)) + (setf (av col) (aref fields-av i)) + (ensure-ucol-datatype col (datatype-for-colname (col col))))))))))) + +(defun ufiles-to-measure () + "Returns a list of ufiles to measure" + (loop for ufile in *umls-files* + unless (or (char= #\M (schar (fil ufile) 0)) + (char= #\m (schar (fil ufile) 0))) + collect ufile)) +(defun ufiles-field-lengths (ufiles) + "Returns a list of lists of containing (FILE MAX AV)" + (loop for ufile in ufiles collect (file-field-lengths ufile))) + +(defun file-field-lengths (ufile) + "Returns a list of FILENAME MAX AV" + (declare (optimize (speed 3) (safety 0))) + (let (fields-max fields-av num-fields (count-lines 0)) + (declare (fixnum count-lines)) + (with-umls-ufile (line ufile) + (unless num-fields + (setq num-fields (length line)) + (setq fields-max (make-array num-fields :element-type 'fixnum + :initial-element 0)) + (setq fields-av (make-array num-fields :element-type '(or integer float) + :initial-element 0))) + (dotimes (i (or num-fields 0)) + (declare (fixnum i)) + (let* ((str (nth i line)) + (len (length #-(and clisp unicode) str + #+(and clisp unicode) + (if *octet-sql-storage* + (ext:convert-string-to-bytes str charset:utf-8) + str)))) + #-(and clisp unicode) (declare (string str)) + (declare (type (integer 0 100000000) len)) + (incf (aref fields-av i) len) + (when (> len (aref fields-max i)) + (setf (aref fields-max i) len)))) + (incf count-lines)) + (dotimes (i (or num-fields 0)) + (setf (aref fields-av i) + (if (plusp count-lines) + (float (/ (aref fields-av i) count-lines)) + 0))) + (list (fil ufile) fields-max fields-av count-lines))) + ;;; UMLS column/file functions -(defun find-col-in-columns (colname filename cols) +(defun find-ucol-of-colname (colname filename ucols) "Returns list of umls-col structure for a column name and a filename" - (dolist (col cols) - (when (and (string-equal filename (fil col)) - (string-equal colname (col col))) - (return-from find-col-in-columns col))) - nil) - -(defun find-or-make-col-in-columns (colname filename cols) - (let ((col (find-col-in-columns colname filename cols))) - (if col - col - ;; try to find column name without a terminal digit - (let* ((last-char (char colname (1- (length colname)))) - (digit (- (char-code last-char) (char-code #\0)))) - (if (and (>= digit 0) (<= digit 9)) - (let ((base-colname (subseq colname 0 (1- (length colname))))) - (setq col (find-col-in-columns base-colname filename cols)) - (if col - (let ((new-col (make-instance 'ucol - :col (copy-seq colname) - :des (copy-seq (des col)) - :ref (copy-seq (ref col)) - :min (cmin col) - :max (cmax col) - :fil (copy-seq (fil col)) - :sqltype (copy-seq (sqltype col)) - :dty (copy-seq (dty col)) - :parse-fun (parse-fun col) - :quotechar (copy-seq (quotechar col)) - :datatype (datatype col) - :custom-value-fun (custom-value-fun col)))) - (push new-col *umls-cols*) - new-col) - (error "Couldn't find a base column for col ~A in file ~A" - colname filename))) - (let ((new-col (make-instance 'ucol - :col (copy-seq colname) - :des "Unknown" - :ref "" - :min nil - :max nil - :fil filename - :sqltype "VARCHAR" - :dty nil - :parse-fun #'add-sql-quotes - :quotechar "'" - :datatype nil - :custom-value-fun nil))) - (push new-col *umls-cols*) - new-col)))))) + (dolist (ucol ucols nil) + (when (and (string-equal filename (fil ucol)) + (string-equal colname (col ucol))) + (return-from find-ucol-of-colname ucol)))) + +(defun ensure-col-in-columns (colname filename ucols) + (aif (find-ucol-of-colname colname filename ucols) + it + (add-ucols (make-ucol-for-column colname filename ucols)))) + +(defun make-ucol-for-column (colname filename ucols) + ;; try to find column name without a terminal digit + (let* ((len (length colname)) + (last-digit? (digit-char-p (schar colname (1- len)))) + (base-colname (if last-digit? + (subseq colname 0 (1- len)) + colname)) + (ucol (when last-digit? + (find-ucol-of-colname base-colname filename ucols)))) + (when (and last-digit? (null ucol)) + (error "Couldn't find a base column for col ~A in file ~A" + colname filename)) + (copy-or-new-ucol colname filename ucol))) + +(defun copy-or-new-ucol (colname filename ucol) + (if ucol + (make-instance + 'ucol + :col (copy-seq colname) :des (copy-seq (des ucol)) :ref (copy-seq (ref ucol)) + :min (cmin ucol) :max (cmax ucol) :fil (copy-seq (fil ucol)) + :sqltype (copy-seq (sqltype ucol)) :dty (copy-seq (dty ucol)) + :parse-fun (parse-fun ucol) :quote-str (copy-seq (quote-str ucol)) + :datatype (datatype ucol) :custom-value-fun (custom-value-fun ucol)) + (make-empty-ucol colname filename))) + +(defun ensure-compiled-fun (fun) + "Ensure that a function is compiled" + (etypecase fun + (null + nil) + (function + (if (compiled-function-p fun) + fun + (compile nil fun))) + (list + (compile nil fun)))) + +(defun make-ucol (col des ref min av max fil dty + &key (sqltype "VARCHAR") (parse-fun #'add-sql-quotes) + (quote-str "'") (custom-value-fun)) + (let ((ucol (make-instance + 'ucol + :col col :des des :ref ref :min min :av av + :max (if (eql max 0) 1 max) ;; ensure at least one char wide + :fil fil + :dty dty + :sqltype sqltype + :quote-str quote-str + :parse-fun (ensure-compiled-fun parse-fun) + :custom-value-fun (ensure-compiled-fun custom-value-fun)))) + (ensure-ucol-datatype ucol (datatype-for-colname col)) + ucol)) + +(defun make-empty-ucol (colname filename) + ;;(format "call in make-empty-ucol: ~A/~A" colname filename) + (make-ucol (copy-seq colname) "Unknown" "" nil nil nil filename nil)) (defun find-ucol (colname filename) "Returns list of umls-col structure for a column name and a filename" - (find-or-make-col-in-columns colname filename *umls-cols*)) + (ensure-col-in-columns colname filename *umls-cols*)) (defun find-ufile (filename) - "Returns umls-file structure for a filename" - (find-if (lambda (f) (string-equal filename (fil f))) *umls-files*)) + "Returns umls-file structure for a filename" + (find-if #'(lambda (f) (string= filename (fil f))) *umls-files*)) + +(defun position-field-file (filename fieldname) + "Returns the position of a field in a file" + (let ((ufile (find-ufile filename))) + (unless ufile + (warn "Unable to find ufile for filename ~A." filename) + (return-from position-field-file nil)) + (let ((pos (position fieldname (fields ufile) :test #'string=))) + (unless pos + (warn "Unable to find field ~A in ufile ~S." fieldname ufile) + (return-from position-field-file nil)) + pos))) + +(defun find-ucols-for-ufile (ufile) + "Returns list of umls-cols for a file structure" + (loop for colname in (fields ufile) + collect (find-ucol colname + (if (subdir ufile) + (concatenate 'string (subdir ufile) "/" (fil ufile)) + (fil ufile))))) + +(defun umls-field-string-to-list (fmt) + "Converts a comma delimited list of fields into a list of field names. Will +append a unique number (starting at 2) onto a column name that is repeated in the list" + (let ((col-counts (make-hash-table :test 'equal))) + (loop for colname in (delimited-string-to-list (escape-column-name fmt) #\,) + collect + (multiple-value-bind (value found) (gethash colname col-counts) + (cond + (found + (incf (gethash colname col-counts)) + (concatenate 'string colname (write-to-string (1+ value)))) + (t + (setf (gethash colname col-counts) 1) + colname)))))) + +(defun decompose-fil (fil) + (if fil + (let ((pos (position #\/ fil))) + (if pos + (values (subseq fil (1+ pos)) (subseq fil 0 pos)) + (values fil nil))) + (values nil nil))) + +(defun filename-to-tablename (file) + (let ((pos (search ".RRF" file))) + (when pos + (setf file (subseq file 0 pos)))) + (substitute #\_ #\. file)) + +(defun make-ufile (dir fil des cls rws bts fields) + (multiple-value-bind (file subdir) (decompose-fil fil) + (let ((ufile (make-instance 'ufile :dir dir :fil file :subdir subdir + :des des :cls cls + :rws rws :bts bts :fields fields + :table (filename-to-tablename file)))) + ufile))) + +(defun set-ucols-for-ufiles (ufiles) + (dolist (ufile ufiles) + (setf (ucols ufile) (find-ucols-for-ufile ufile)))) + +(defun datatype-for-colname (colname) +"Return datatype for column name" + (second (find colname +col-datatypes+ :key #'car :test #'string-equal))) + +(defun canonicalize-column-type (type) + (cond + ((string-equal type "TINYINT") + (case *umls-sql-type* + (:mysql "TINYINT") + ((:postgresql :postgresql-socket) "INT1") + (:oracle "NUMBER(3,0)") + (t "INTEGER"))) + ((string-equal type "SMALLINT") + (case *umls-sql-type* + (:mysql "SMALLINT") + ((:postgresql :postgresql-socket) "INT2") + (:oracle "NUMBER(5,0)") + (t "INTEGER"))) + ((string-equal type "INTEGER") + (case *umls-sql-type* + (:mysql "INTEGER") + ((:postgresql :postgresql-socket) "INT4") + (:oracle "NUMBER(9,0)") + (t "INTEGER"))) + ((string-equal type "BIGINT") + (case *umls-sql-type* + (:mysql "BIGINT") + ((:postgresql :postgresql-socket) "INT8") + (:oracle "NUMBER(38,0)") + (t "INTEGER"))) + ((string-equal type "TEXT") + (case *umls-sql-type* + (:mysql "TEXT") + ((:postgresql :postgresql-socket) "TEXT") + (:oracle "VARCHAR2(3000)") + (t "VARCHAR(3000)"))) + ((string-equal type "VARCHAR") + (case *umls-sql-type* + (:mysql "VARCHAR") + ((:postgresql :postgresql-socket) "VARCHAR") + (:oracle "VARCHAR2") + (t "VARCHAR"))) + ((string-equal type "NUMERIC") + (case *umls-sql-type* + (:mysql "NUMERIC") + ((:postgresql :postgresql-socket) "NUMERIC") + (:oracle "NUMBER") + (t "NUMERIC"))) + (t + type))) -(defun ucols-for-ufile (file) - "Returns list of umls-cols for a file structure" - (let ((filename (fil file))) - (mapcar (lambda (col) (find-ucol col filename)) - (fields file)))) +(defun ensure-ucol-datatype (col datatype) + "Add data type information to column" + (setf (datatype col) datatype) + (case datatype + (sql-u (setf (sqltype col) (canonicalize-column-type "INTEGER") + (parse-fun col) #'parse-ui + (quote-str col) "")) + (sql-s (setf (sqltype col) (canonicalize-column-type "SMALLINT") + (parse-fun col) #'parse-integer + (quote-str col) "")) + (sql-l (setf (sqltype col) (canonicalize-column-type "BIGINT") + (parse-fun col) #'parse-integer + (quote-str col) "")) + (sql-i (setf (sqltype col) (canonicalize-column-type "INTEGER") + (parse-fun col) #'parse-integer + (quote-str col) "")) + (sql-t (setf (sqltype col) (canonicalize-column-type "TINYINT") + (parse-fun col) #'parse-integer + (quote-str col) "")) + (sql-f (setf (sqltype col) (canonicalize-column-type "NUMERIC") + (parse-fun col) #'read-from-string + (quote-str col) "")) + (t ; Default column type, optimized text storage + (setf (parse-fun col) #'add-sql-quotes + (quote-str col) "'") + (when (and (cmax col) (av col)) + (if (> (cmax col) 255) + (setf (sqltype col) (canonicalize-column-type "TEXT")) + (setf (sqltype col) (canonicalize-column-type "VARCHAR"))))))) +(defun escape-column-name (name) + (substitute #\_ #\/ name)) +;; SQLNAME is required for collision of SQL reserved words (MYSQL 8: RANK) +;; and column names in UMLS (RANK in MRRANK) +(defvar *sql-reserved-names* '("RANK")) +(defmethod sqlname ((c ucol)) + (sqlname (col c))) +(defmethod sqlname ((name string)) + (if (find name *sql-reserved-names* :test #'string-equal) + (concatenate 'string "_" name) + name)) +(defmethod sqlname ((l list)) + (mapcar #'sqlname l)) +(defmethod sqlname ((s symbol)) + (sqlname (symbol-name s)))