ob-stata.el: new file for stata code evaluation

* contrib/lisp/ob-stata.el: New file based on ob-julia.el.
* contrib/README: Document addition of new file.

ob-stata.el provides basic support for evaluating Stata code.

contrib/README

@@ -80,6 +80,7 @@ ob-fomus.el        	 --- Org-babel functions for fomus evaluation
 ob-julia.el  	 	 --- Org-babel functions for julia evaluation
 ob-mathomatic.el   	 --- Org-babel functions for mathomatic evaluation
 ob-oz.el           	 --- Org-babel functions for Oz evaluation
+ob-stata.el              --- Org-babel functions for Stata evaluation
 ob-tcl.el 		 --- Org-babel functions for tcl evaluation
 
 External libraries

contrib/lisp/ob-stata.el

@@ -0,0 +1,313 @@
+;;; ob-stata.el --- org-babel functions for stata code evaluation
+
+;; Copyright (C) 2014 Ista Zahn
+;; Author: Ista Zahn istazahn@gmail.com
+;;      G. Jay Kerns
+;;      Eric Schulte
+;;      Dan Davison
+
+
+;; This file is not part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+
+;; The file provides Org-Babel support for evaluating stata code.
+;; It is basically result of find-and-replace "stata" for "julia"
+;; in ob-julia.el by G. Jay Kerns. Only ":results output" works: the
+;; header args must include ":results output" (this is the default).
+;; Note that I'm not sure ':results value' makes sense or is useful 
+;; but I have left all the value-processing stuff inherited from 
+;; ob-julia and ob-R. ':results graphics' would be nice, but I have
+;; not tried to implement it. 
+;; --Ista, 07/30/2014
+
+;;; Requirements:
+;; Stata: http://stata.com
+;; ESS: http://ess.r-project.org
+
+;;; Code:
+(require 'ob)
+(eval-when-compile (require 'cl))
+
+(declare-function orgtbl-to-csv "org-table" (table params))
+(declare-function stata "ext:ess-stata" (&optional start-args))
+(declare-function inferior-ess-send-input "ext:ess-inf" ())
+(declare-function ess-make-buffer-current "ext:ess-inf" ())
+(declare-function ess-eval-buffer "ext:ess-inf" (vis))
+(declare-function org-number-sequence "org-compat" (from &optional to inc))
+(declare-function org-remove-if-not "org" (predicate seq))
+
+(defconst org-babel-header-args:stata
+  '((width		 . :any)
+    (horizontal		 . :any)
+    (results             . ((file list vector table scalar verbatim)
+			    (raw org html latex code pp wrap)
+			    (replace silent append prepend)
+                            ;; NOTE: not sure 'value' makes sense in stata
+                            ;; we may want to remove it from the list
+			    (output value graphics))))
+  "stata-specific header arguments.")
+
+(add-to-list 'org-babel-tangle-lang-exts '("stata" . "do"))
+
+;; only ':results output' currently works, so make that the default
+(defvar org-babel-default-header-args:stata '((:results . "output")))
+
+(defcustom org-babel-stata-command inferior-STA-program-name
+  "Name of command to use for executing stata code."
+  :group 'org-babel
+  :version "24.4"
+  :package-version '(Org . "8.3")
+  :type 'string)
+
+(defvar ess-local-process-name) ; dynamically scoped
+(defun org-babel-edit-prep:stata (info)
+  (let ((session (cdr (assoc :session (nth 2 info)))))
+    (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
+      (save-match-data (org-babel-stata-initiate-session session nil)))))
+
+(defun org-babel-expand-body:stata (body params &optional graphics-file)
+  "Expand BODY according to PARAMS, return the expanded body."
+  (let ((graphics-file
+	 (or graphics-file (org-babel-stata-graphical-output-file params))))
+    (mapconcat
+     #'identity
+     ((lambda (inside)
+	(if graphics-file
+            inside
+	  inside))
+      (append (org-babel-variable-assignments:stata params)
+	      (list body))) "\n")))
+
+(defun org-babel-execute:stata (body params)
+  "Execute a block of stata code.
+This function is called by `org-babel-execute-src-block'."
+  (save-excursion
+    (let* ((result-params (cdr (assoc :result-params params)))
+	   (result-type (cdr (assoc :result-type params)))
+           (session (org-babel-stata-initiate-session
+		     (cdr (assoc :session params)) params))
+	   (colnames-p (cdr (assoc :colnames params)))
+	   (rownames-p (cdr (assoc :rownames params)))
+	   (graphics-file (org-babel-stata-graphical-output-file params))
+	   (full-body (org-babel-expand-body:stata body params graphics-file))
+	   (result
+	    (org-babel-stata-evaluate
+	     session full-body result-type result-params
+	     (or (equal "yes" colnames-p)
+		 (org-babel-pick-name
+		  (cdr (assoc :colname-names params)) colnames-p))
+	     (or (equal "yes" rownames-p)
+		 (org-babel-pick-name
+		  (cdr (assoc :rowname-names params)) rownames-p)))))
+      (if graphics-file nil result))))
+
+(defun org-babel-prep-session:stata (session params)
+  "Prepare SESSION according to the header arguments specified in PARAMS."
+  (let* ((session (org-babel-stata-initiate-session session params))
+	 (var-lines (org-babel-variable-assignments:stata params)))
+    (org-babel-comint-in-buffer session
+      (mapc (lambda (var)
+              (end-of-line 1) (insert var) (comint-send-input nil t)
+              (org-babel-comint-wait-for-output session)) var-lines))
+    session))
+
+(defun org-babel-load-session:stata (session body params)
+  "Load BODY into SESSION."
+  (save-window-excursion
+    (let ((buffer (org-babel-prep-session:stata session params)))
+      (with-current-buffer buffer
+        (goto-char (process-mark (get-buffer-process (current-buffer))))
+        (insert (org-babel-chomp body)))
+      buffer)))
+
+;; helper functions
+
+(defun org-babel-variable-assignments:stata (params)
+  "Return list of stata statements assigning the block's variables."
+  (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
+    (mapcar
+     (lambda (pair)
+       (org-babel-stata-assign-elisp
+	(car pair) (cdr pair)
+	(equal "yes" (cdr (assoc :colnames params)))
+	(equal "yes" (cdr (assoc :rownames params)))))
+     (mapcar
+      (lambda (i)
+	(cons (car (nth i vars))
+	      (org-babel-reassemble-table
+	       (cdr (nth i vars))
+	       (cdr (nth i (cdr (assoc :colname-names params))))
+	       (cdr (nth i (cdr (assoc :rowname-names params)))))))
+      (org-number-sequence 0 (1- (length vars)))))))
+
+(defun org-babel-stata-quote-csv-field (s)
+  "Quote field S for export to stata."
+  (if (stringp s)
+      (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
+    (format "%S" s)))
+
+(defun org-babel-stata-assign-elisp (name value colnames-p rownames-p)
+  "Construct stata code assigning the elisp VALUE to a variable named NAME."
+  (if (listp value)
+      (let ((max (apply #'max (mapcar #'length (org-remove-if-not
+						#'sequencep value))))
+	    (min (apply #'min (mapcar #'length (org-remove-if-not
+						#'sequencep value))))
+	    (transition-file (org-babel-temp-file "stata-import-")))
+        ;; ensure VALUE has an orgtbl structure (depth of at least 2)
+        (unless (listp (car value)) (setq value (list value)))
+        (with-temp-file transition-file
+          (insert
+	   (orgtbl-to-csv value '(:fmt org-babel-stata-quote-csv-field))
+	   "\n"))
+	(let ((file (org-babel-process-file-name transition-file 'noquote))
+	      (header (if (or (eq (nth 1 value) 'hline) colnames-p)
+			  "TRUE" "FALSE"))
+	      (row-names (if rownames-p "1" "NULL")))
+	  (if (= max min)
+	      (format "%s = insheet using \"%s\"" name file)
+	    (format "%s = insheet using \"%s\""
+		    name file))))
+    (format "%s = %s" name (org-babel-stata-quote-csv-field value))))
+
+(defvar ess-ask-for-ess-directory) ; dynamically scoped
+
+(defun org-babel-stata-initiate-session (session params)
+  "If there is not a current stata process then create one."
+  (unless (string= session "none")
+    (let ((session (or session "*stata*"))
+	  (ess-ask-for-ess-directory
+	   (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
+		(not (cdr (assoc :dir params))))))
+      (if (org-babel-comint-buffer-livep session)
+	  session
+	(save-window-excursion
+	  (require 'ess) (stata)
+	  (rename-buffer
+	   (if (bufferp session)
+	       (buffer-name session)
+	     (if (stringp session)
+		 session
+	       (buffer-name))))
+	  (current-buffer))))))
+
+(defun org-babel-stata-associate-session (session)
+  "Associate stata code buffer with a stata session.
+Make SESSION be the inferior ESS process associated with the
+current code buffer."
+  (setq ess-local-process-name
+	(process-name (get-buffer-process session)))
+  (ess-make-buffer-current))
+
+(defun org-babel-stata-graphical-output-file (params)
+  "Name of file to which stata should send graphical output."
+  (and (member "graphics" (cdr (assq :result-params params)))
+       (cdr (assq :file params))))
+
+(defvar org-babel-stata-eoe-indicator "display \"org_babel_stata_eoe\"")
+(defvar org-babel-stata-eoe-output "org_babel_stata_eoe")
+
+(defvar org-babel-stata-write-object-command "outsheet using \"%s\"")
+
+(defun org-babel-stata-evaluate
+  (session body result-type result-params column-names-p row-names-p)
+  "Evaluate stata code in BODY."
+  (if session
+      (org-babel-stata-evaluate-session
+       session body result-type result-params column-names-p row-names-p)
+    (org-babel-stata-evaluate-external-process
+     body result-type result-params column-names-p row-names-p)))
+
+(defun org-babel-stata-evaluate-external-process
+  (body result-type result-params column-names-p row-names-p)
+  "Evaluate BODY in external stata process.
+If RESULT-TYPE equals 'output then return standard output as a
+string.  If RESULT-TYPE equals 'value then return the value of the
+last statement in BODY, as elisp."
+  (case result-type
+    (value
+     (let ((tmp-file (org-babel-temp-file "stata-")))
+       (org-babel-eval org-babel-stata-command
+		       (format org-babel-stata-write-object-command
+			       (org-babel-process-file-name tmp-file 'noquote)
+			       (format "begin\n%s\nend" body)))
+       (org-babel-stata-process-value-result
+	(org-babel-result-cond result-params
+	  (with-temp-buffer
+	    (insert-file-contents tmp-file)
+	    (buffer-string))
+	  (org-babel-import-elisp-from-file tmp-file '(4)))
+	column-names-p)))
+    (output (org-babel-eval org-babel-stata-command body))))
+
+(defun org-babel-stata-evaluate-session
+  (session body result-type result-params column-names-p row-names-p)
+  "Evaluate BODY in SESSION.
+If RESULT-TYPE equals 'output then return standard output as a
+string.  If RESULT-TYPE equals 'value then return the value of the
+last statement in BODY, as elisp."
+  (case result-type
+    (value
+     (with-temp-buffer
+       (insert (org-babel-chomp body))
+       (let ((ess-local-process-name
+	      (process-name (get-buffer-process session)))
+	     (ess-eval-visibly-p nil))
+	 (ess-eval-buffer nil)))
+     (let ((tmp-file (org-babel-temp-file "stata-")))
+       (org-babel-comint-eval-invisibly-and-wait-for-file
+	session tmp-file
+	(format org-babel-stata-write-object-command
+		(org-babel-process-file-name tmp-file 'noquote) "ans"))
+       (org-babel-stata-process-value-result
+	(org-babel-result-cond result-params
+	  (with-temp-buffer
+	    (insert-file-contents tmp-file)
+	    (buffer-string))
+	  (org-babel-import-elisp-from-file tmp-file '(4)))
+	column-names-p)))
+    (output
+     (mapconcat
+      #'org-babel-chomp
+      (butlast
+       (delq nil
+	     (mapcar
+	      (lambda (line) (when (> (length line) 0) line))
+	      (mapcar
+	       (lambda (line) ;; cleanup extra prompts left in output
+		 (if (string-match
+		      "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
+		     (substring line (match-end 1))
+		   line))
+	       (org-babel-comint-with-output (session org-babel-stata-eoe-output)
+		 (insert (mapconcat #'org-babel-chomp
+				    (list body org-babel-stata-eoe-indicator)
+				    "\n"))
+		 (inferior-ess-send-input)))))) "\n"))))
+
+(defun org-babel-stata-process-value-result (result column-names-p)
+  "stata-specific processing of return value.
+Insert hline if column names in output have been requested."
+  (if column-names-p
+      (cons (car result) (cons 'hline (cdr result)))
+    result))
+
+(provide 'ob-stata)
+
+;;; ob-stata.el ends here