--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: parse-common.lisp
+;;;; Purpose: Common, stable parsing routines 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 ensure-ucols+ufiles (&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 with an optional extension"
+ (etypecase filename
+ (string
+ (merge-pathnames
+ (make-pathname :name (concatenate 'string filename extension))
+ (case (schar filename 0)
+ ((#\M #\m)
+ *meta-path*)
+ ((#\L #\l)
+ *lex-path*)
+ ((#\S #\s)
+ *net-path*)
+ (t
+ *umls-path*))))
+ (pathname
+ 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 ensure-field-lengths ()
+ "Initial colstruct field lengths for files that don't have a measurement.
+Currently, these are the LEX and NET files."
+ (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" filename))
+ (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 (fil ufile))))
+
+(defun file-field-lengths (filename)
+ "Returns a list of FILENAME MAX AV"
+ (declare (optimize (speed 3) (safety 0)))
+ (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-ucol-of-colname (colname filename ucols)
+"Returns list of umls-col structure for a column name and a filename"
+ (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"
+ (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 find-ucols-for-ufile (ufile)
+ "Returns list of umls-cols for a file structure"
+ (loop for colname in (fields ufile)
+ collect (find-ucol colname (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 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-ufile ufile))
+ 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")
+ (setf (sqltype col) "VARCHAR"))))))
+
+(defun escape-column-name (name)
+ (substitute #\_ #\/ name))
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