X-Git-Url: http://git.kpe.io/?p=umlisp-orf.git;a=blobdiff_plain;f=parse-common.lisp;fp=parse-common.lisp;h=6c82346721842bc0c66773154c979ca7e2f7d4e9;hp=5931b0583dd539a84237ffdbaa5e68eb87d79219;hb=1e348ab8a58095fafac025161fc172626c466949;hpb=d8ba6e3d4c5713fd1629317022cec8150340545a diff --git a/parse-common.lisp b/parse-common.lisp index 5931b05..6c82346 100644 --- a/parse-common.lisp +++ b/parse-common.lisp @@ -39,17 +39,17 @@ "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*) - ((#\L #\l) - *lex-path*) - ((#\S #\s) - *net-path*) - (t - *umls-path*)))) + ((#\M #\m) + *meta-path*) + ((#\L #\l) + *lex-path*) + ((#\S #\s) + *net-path*) + (t + *umls-path*)))) (pathname filename))) @@ -57,8 +57,8 @@ "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)))) + eof + (delimited-string-to-list line #\| t)))) ;;; Find field lengths for LEX and NET files @@ -68,30 +68,30 @@ 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))))))))) - + (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)) - - + 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)))) @@ -102,17 +102,17 @@ Currently, these are the LEX and NET files." (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))) + (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)))) + (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)))) @@ -124,7 +124,7 @@ Currently, these are the LEX and NET files." "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))) + (string-equal colname (col ucol))) (return-from find-ucol-of-colname ucol)))) (defun ensure-col-in-columns (colname filename ucols) @@ -135,15 +135,15 @@ Currently, these are the LEX and NET files." (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)))) + (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)) + colname filename)) (copy-or-new-ucol colname filename ucol))) (defun copy-or-new-ucol (colname filename ucol) @@ -164,22 +164,22 @@ Currently, these are the LEX and NET files." nil) (function (if (compiled-function-p fun) - fun - (compile nil 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)) + &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)))) + '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)) @@ -192,37 +192,37 @@ Currently, these are the LEX and NET files." (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 (fil 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)))))) + 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))) + :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" +"Return datatype for column name" (second (find colname +col-datatypes+ :key #'car :test #'string-equal))) (defun ensure-ucol-datatype (col datatype) @@ -230,27 +230,27 @@ append a unique number (starting at 2) onto a column name that is repeated in th (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) "'") + (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")))))) + (setf (sqltype col) "TEXT") + (setf (sqltype col) "VARCHAR")))))) (defun escape-column-name (name) (substitute #\_ #\/ name))