(defmethod fmt-cui ((c ucon))
(fmt-cui (cui c)))
-(defmethod fmt-cui ((c fixnum))
- (prefixed-fixnum-string c #\C 7))
+(when *has-fixnum-class*
+ (defmethod fmt-cui ((c fixnum))
+ (prefixed-fixnum-string c #\C 7)))
+
+(defmethod fmt-cui ((c integer))
+ (prefixed-integer-string c #\C 7))
(defmethod fmt-cui ((c string))
(if (eql (aref c 0) #\C)
(defmethod fmt-lui ((l uterm))
(fmt-lui (lui l)))
-(defmethod fmt-lui ((l fixnum))
- (prefixed-fixnum-string l #\L 7))
+(when *has-fixnum-class*
+ (defmethod fmt-lui ((l fixnum))
+ (prefixed-fixnum-string l #\L 7)))
+
+(defmethod fmt-lui ((l integer))
+ (prefixed-integer-string l #\L 7))
(defmethod fmt-lui ((l string))
(if (eql (aref l 0) #\L)
(defmethod fmt-sui ((s ustr))
(fmt-sui (sui s)))
-(defmethod fmt-sui ((s fixnum))
- (prefixed-fixnum-string s #\S 7))
+(when *has-fixnum-class*
+ (defmethod fmt-sui ((s fixnum))
+ (prefixed-fixnum-string s #\S 7)))
+
+(defmethod fmt-sui ((s integer))
+ (prefixed-integer-string s #\S 7))
(defmethod fmt-sui ((s string))
(if (eql (aref s 0) #\S)
(fmt-sui (parse-integer s))))
(defgeneric fmt-tui (tui))
-(defmethod fmt-tui ((tui fixnum))
- (prefixed-fixnum-string tui #\T 3))
+(when *has-fixnum-class*
+ (defmethod fmt-tui ((tui fixnum))
+ (prefixed-fixnum-string tui #\T 3)))
+
+(defmethod fmt-tui ((tui integer))
+ (prefixed-integer-string tui #\T 3))
(defmethod fmt-tui ((tui string))
(if (eql (aref tui 0) #\T)
(fmt-tui (parse-integer tui))))
(defgeneric fmt-aui (aui))
-(defmethod fmt-aui ((aui fixnum))
- (prefixed-fixnum-string aui #\A 7))
+(when *has-fixnum-class*
+ (defmethod fmt-aui ((aui fixnum))
+ (prefixed-fixnum-string aui #\A 7)))
+
+(defmethod fmt-aui ((aui integer))
+ (prefixed-integer-string aui #\A 7))
(defmethod fmt-aui ((aui string))
(if (eql (aref aui 0) #\A)
(fmt-aui (parse-integer aui))))
(defgeneric fmt-eui (e))
-(defmethod fmt-eui ((e fixnum))
- (prefixed-fixnum-string e #\E 7))
+(when *has-fixnum-class*
+ (defmethod fmt-eui ((e fixnum))
+ (prefixed-fixnum-string e #\E 7)))
+
+(defmethod fmt-eui ((e integer))
+ (prefixed-integer-string e #\E 7))
(defmethod fmt-eui ((e string))
(if (eql (aref e 0) #\E)
;;; Paths for files
(defparameter *umls-path*
- (make-pathname :directory '(:absolute "home" "kevin" "2006AC"))
+ (make-pathname :directory '(:absolute "srv" "umls" "2006AC"))
"Path for base of UMLS data files")
-(defvar *meta-path*
- (merge-pathnames
+(defparameter *meta-path*
+ (merge-pathnames
(make-pathname :directory '(:relative "META"))
*umls-path*))
-(defvar *lex-path*
- (merge-pathnames
+(defparameter *lex-path*
+ (merge-pathnames
(make-pathname :directory '(:relative "LEX"))
*umls-path*))
-(defvar *net-path*
- (merge-pathnames
+(defparameter *net-path*
+ (merge-pathnames
(make-pathname :directory '(:relative "NET"))
*umls-path*))
;;; Structures for parsing UMLS text files
-
-(defparameter *umls-files* nil
+
+(defparameter *umls-files* nil
"List of umls file structures. Used when parsing text files.")
-(defparameter *umls-cols* nil
+(defparameter *umls-cols* nil
"List of meta column structures. Used when parsing text files.")
+;; Special variables
+
+(defvar *has-fixnum-class* (when (ignore-errors (find-class 'fixnum)) t))
+
+(defvar *octet-sql-storage* t
+ "Used to deciding field lengths. Use nil if using UTF-8 database encoding. But, UTF-8 will cause MySQL to double the bytes used for fixed field sizes.")
+
;; Preliminary objects to replace structures
(defclass ufile ()
(format s "~A" (col obj))))
-
+cl-umlisp (4.2.0-1) unstable; urgency=low
+
+ * Add support for UMLS 2006AC
+
+ -- Kevin M. Rosenberg <kmr@debian.org> Sun, 3 Sep 2006 23:38:27 -0600
+
cl-umlisp (4.1.0-2) unstable; urgency=low
* New upstream URI
(defun ensure-ucols+ufiles (&optional (alwaysclear nil))
"Initialize all UMLS file and column structures if not already initialized"
- (when (or alwaysclear (null *umls-files*))
- (setq *umls-cols* nil)
- (setq *umls-files* nil)
- (gen-ucols)
- (gen-ufiles)
- (ensure-field-lengths)))
+ (handler-case
+ (when (or alwaysclear (null *umls-files*))
+ (setf *umls-cols* nil *umls-files* nil)
+ (gen-ucols)
+ (gen-ufiles)
+ (ensure-field-lengths))
+ (error (e)
+ (setf *umls-cols* nil *umls-files* nil)
+ (error e)))
+ t)
+
(defun add-ucols (ucols)
"Adds a ucol or list of ucols to *umls-cols*. Returns input value."
(defun ufile-pathname (ufile &optional (extension ""))
"Return pathname for a umls filename with an optional extension"
(assert (typep ufile 'ufile))
- (let ((dirs (append (list (dir ufile))
+ (let ((dirs (append (list (dir ufile))
(awhen (subdir ufile) (list it)))))
- (merge-pathnames
+ (merge-pathnames
(make-pathname :name (concatenate 'string (fil ufile) extension)
:directory (cons :relative dirs))
*umls-path*)))
"Return pathname for a umls filename with an optional extension"
(etypecase filename
(string
- (merge-pathnames
- (make-pathname :name (concatenate 'string filename extension))
+ (merge-pathnames
+ (make-pathname :name (concatenate 'string filename extension))
(case (schar filename 0)
((#\M #\m)
*meta-path*)
(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"
+ "Number of file fields ~A not equal to field count in ufile ~S"
fields-max file))
(dotimes (i (length (fields file)))
(declare (fixnum i))
(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)))
(with-umls-ufile (line ufile)
(unless num-fields
(setq num-fields (length line))
- (setq fields-max (make-array num-fields :element-type 'fixnum
+ (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))))
+ (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))))
(incf (aref fields-av i) len)
(when (> len (aref fields-max i))
(setf (aref fields-max i) len))))
(quote-str "'") (custom-value-fun))
(let ((ucol (make-instance
'ucol
- :col col :des des :ref ref :min min :av av
+ :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
+ :sqltype sqltype
:quote-str quote-str
:parse-fun (ensure-compiled-fun parse-fun)
:custom-value-fun (ensure-compiled-fun custom-value-fun))))
(ensure-col-in-columns colname filename *umls-cols*))
(defun find-ufile (filename)
- "Returns umls-file structure for a 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
+ collect (find-ucol colname
(if (subdir ufile)
(concatenate 'string (subdir ufile) "/" (fil ufile))
(fil ufile)))))
ufile)))
(defun datatype-for-colname (colname)
-"Return datatype for column name"
+"Return datatype for column name"
(second (find colname +col-datatypes+ :key #'car :test #'string-equal)))
(defun canonicalize-column-type (type)
(t "NUMERIC")))
(t
type)))
-
+
(defun ensure-ucol-datatype (col datatype)
"Add data type information to column"
(setf (datatype col) datatype)
(parse-fun col) #'read-from-string
(quote-str col) ""))
(t ; Default column type, optimized text storage
- (setf (parse-fun col) #'add-sql-quotes
+ (setf (parse-fun col) #'add-sql-quotes
(quote-str col) "'")
(when (and (cmax col) (av col))
(if (> (cmax col) 255)
(delimited-string-to-list line #\| t))))
(defun source-files (path)
- (if (probe-file path)
+ (if (probe-file path)
(list path)
(sort
(directory (make-pathname :defaults path
`(let ((,eof (gensym "EOFSYM-"))
(,buffer (make-fields-buffer))
(,files (source-files ,path)))
- (with-open-file (,ustream (first ,files) :direction :input)
+ (with-open-file (,ustream (first ,files) :direction :input
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
(do ((,line (read-buffered-fields ,buffer ,ustream #\| ,eof)
(read-buffered-fields ,buffer ,ustream #\| ,eof)))
((eq ,line ,eof) t)
(files (gensym "FILES-")))
`(let ((,eof (gensym "EOFSYM-"))
(,files (source-files ,path)))
- (with-open-file (,ustream (first ,files) :direction :input)
- (do ((,line (read-umls-line ,ustream ,eof)
- (read-umls-line ,ustream ,eof)))
- ((eq ,line ,eof) t)
- ,@body)))))
+ (unless ,files
+ (error "Can't find file files for ~A~%" ,path))
+ (with-open-file (,ustream (first ,files) :direction :input
+ #+(and clisp unicode) :external-format
+ #+(and clisp unicode) charset:utf-8)
+ (do ((,line (read-umls-line ,ustream ,eof)
+ (read-umls-line ,ustream ,eof)))
+ ((eq ,line ,eof) t)
+ ,@body)))))
(defmacro with-umls-ufile ((line ufile) &body body)
"Opens a UMLS and processes each parsed line with (body) argument"
(defun make-preparse-hash-table ()
(if sui-lrl-hash
(progn
- (clrhash pfstr-hash)
- (clrhash cui-lrl-hash)
- (clrhash lui-lrl-hash)
- (clrhash sui-lrl-hash)
- (clrhash cuisui-lrl-hash)
- (clrhash sab-srl-hash))
+ (clrhash pfstr-hash)
+ (clrhash cui-lrl-hash)
+ (clrhash lui-lrl-hash)
+ (clrhash sui-lrl-hash)
+ (clrhash cuisui-lrl-hash)
+ (clrhash sab-srl-hash))
(setf
pfstr-hash (make-hash-table :size 800000)
cui-lrl-hash (make-hash-table :size 800000)
(defun ensure-preparse (&optional (force-read nil))
(when (or force-read (not *preparse-hash-init?*))
- (make-preparse-hash-table)
- (setq *preparse-hash-init?* t))
+ (make-preparse-hash-table))
(with-umls-file (line "MRCONSO.RRF")
(let ((cui (parse-ui (nth 0 line)))
(lui (parse-ui (nth 3 line)))
(multiple-value-bind (val found) (gethash sab sab-srl-hash)
(declare (ignore val))
(unless found
- (setf (gethash sab sab-srl-hash) srl))))))
+ (setf (gethash sab sab-srl-hash) srl)))))
+ (setq *preparse-hash-init?* t))
(defun pfstr-hash (cui) (gethash cui pfstr-hash))
(defun cui-lrl (cui) (gethash cui cui-lrl-hash))
(defun sql-connect ()
"Connect to UMLS database, automatically used pooled connections"
(clsql:connect (list *umls-sql-host* (lookup-db-name *umls-sql-db*)
- *umls-sql-user* *umls-sql-passwd*)
+ *umls-sql-user* *umls-sql-passwd*)
:database-type *umls-sql-type* :pool t))
(defun sql-disconnect (conn)
projects / umlisp.git / commitdiff