;;;; Author: Kevin M. Rosenberg
;;;; Date Started: Apr 2000
;;;;
-;;;; $Id: parse-common.lisp,v 1.8 2003/05/06 07:44:07 kevin Exp $
+;;;; $Id: parse-common.lisp,v 1.9 2003/05/07 21:57:06 kevin Exp $
;;;;
;;;; This file, part of UMLisp, is
;;;; Copyright (c) 2000-2002 by Kevin M. Rosenberg, M.D.
(eval-when (:compile-toplevel)
(declaim (optimize (speed 3) (safety 1) (compilation-speed 0) (debug 3))))
+(defun ensure-init-umls (&optional (alwaysclear nil))
+"Initialize all UMLS file and column structures if not already initialized"
+ (when (or alwaysclear (null *umls-files*))
+ (gen-ucols)
+ (gen-ufiles)
+ (ensure-field-lengths)))
+
+(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 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
;;; 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) length-list
+ (let ((file (find-ufile filename)))
+ (unless file
+ (error "Can't find ~A filename in ufiles"))
+ (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 (char (fil ufile) 0))
+ (char= #\m (char (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 (fil ufile))))
+
+(defun file-field-lengths (filename)
+ "Returns a list of FILENAME MAX AV"
+ (let (fields-max fields-av num-fields (count-lines 0))
+ (with-umls-file (line filename)
+ (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 'number
+ :initial-element 0)))
+ (dotimes (i num-fields)
+ (declare (fixnum i))
+ (let ((len (length (nth i line))))
+ (incf (aref fields-av i) len)
+ (when (> len (aref fields-max i))
+ (setf (aref fields-max i) len))))
+ (incf count-lines))
+ (dotimes (i num-fields)
+ (setf (aref fields-av i) (float (/ (aref fields-av i) count-lines))))
+ (list filename fields-max fields-av)))
;;; 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 (char 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 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 max :fil fil
+ :dty dty :sqltype sqltype :parse-fun parse-fun
+ :quote-str quote-str :custom-value-fun custom-value-fun)))
+ (ensure-ucol-datatype ucol (datatype-for-colname col))
+ ucol))
+
+(defun make-empty-ucol (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*))
-
-(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))))
-
-
+ (find-if #'(lambda (f) (string-equal filename (fil f))) *umls-files*))
+
+(defun find-ucols-for-filename (filename)
+ "Returns list of umls-cols for a file structure"
+ (loop for colname in (fields (find-ufile filename))
+ collect (find-ucol colname filename)))
+
+(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 col col-counts)
+ (cond
+ (found
+ (incf (gethash col col-counts))
+ (concatenate 'string colname (write-to-string (1+ value))))
+ (t
+ (setf (gethash col col-counts) 1)
+ colname))))))
+
+(defun make-ufile (fil des table cls rws bts fields)
+ (let ((ufile
+ (make-instance
+ 'ufile :fil fil :des des :table table :cls cls :rws rws :bts bts
+ :fields fields)))
+ (setf (ucols ufile) (find-ucols-for-filename fil))
+ ufile))
+
+(defun datatype-for-colname (colname)
+"Return datatype for column name"
+ (second (find colname +col-datatypes+ :key #'car :test #'string-equal)))
+
+(defun ensure-ucol-datatype (col datatype)
+"Add data type information to column"
+ (setf (datatype col) datatype)
+ (case datatype
+ (sql-u (setf (sqltype col) "INTEGER"
+ (parse-fun col) #'parse-ui
+ (quote-str col) ""))
+ (sql-s (setf (sqltype col) "SMALLINT"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-l (setf (sqltype col) "BIGINT"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-i (setf (sqltype col) "INTEGER"
+ (parse-fun col) #'parse-integer
+ (quote-str col) ""))
+ (sql-f (setf (sqltype col) "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) "TEXT")
+ (if (< (- (cmax col) (av col)) 4)
+ (setf (sqltype col) "CHAR") ; if average bytes wasted < 4
+ (setf (sqltype col) "VARCHAR")))))))
+
+(defun escape-column-name (name)
+ (substitute #\_ #\/ name))
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