* [PATCH] ob-stata.el: new file for stata code evaluation
@ 2014-07-30 21:19 Ista Zahn
2014-07-31 10:55 ` Bastien
0 siblings, 1 reply; 2+ messages in thread
From: Ista Zahn @ 2014-07-30 21:19 UTC (permalink / raw)
To: emacs-orgmode Mailinglist
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Here is a patch (against master) adding babel support for evaluating
stata code. As discussed in a previous thread[1] there is a lot of
work that should be done to clean it up and make it more useful. It
does work for basic code evaluation, so I'm submitting it here in the
hope that others find it useful.
Best,
Ista
[1] https://lists.gnu.org/archive/html/emacs-orgmode/2014-06/msg00862.html
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From 24d957b8fc3eb207158e94cdec1a362ba2e79ff0 Mon Sep 17 00:00:00 2001
From: Ista Zahn <istazahn@gmail.com>
Date: Wed, 30 Jul 2014 17:07:16 -0400
Subject: [PATCH] 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 | 1 +
contrib/lisp/ob-stata.el | 313 +++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 314 insertions(+)
create mode 100644 contrib/lisp/ob-stata.el
diff --git a/contrib/README b/contrib/README
index 2a67b65..e92da14 100644
--- a/contrib/README
+++ b/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
diff --git a/contrib/lisp/ob-stata.el b/contrib/lisp/ob-stata.el
new file mode 100644
index 0000000..8a70754
--- /dev/null
+++ b/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
--
2.0.3
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] ob-stata.el: new file for stata code evaluation
2014-07-30 21:19 [PATCH] ob-stata.el: new file for stata code evaluation Ista Zahn
@ 2014-07-31 10:55 ` Bastien
0 siblings, 0 replies; 2+ messages in thread
From: Bastien @ 2014-07-31 10:55 UTC (permalink / raw)
To: Ista Zahn; +Cc: emacs-orgmode Mailinglist
Hi Ista,
Ista Zahn <istazahn@gmail.com> writes:
> Here is a patch (against master) adding babel support for evaluating
> stata code. As discussed in a previous thread[1] there is a lot of
> work that should be done to clean it up and make it more useful. It
> does work for basic code evaluation, so I'm submitting it here in the
> hope that others find it useful.
Applied, thanks a lot!
You might also consider adding examples and documentation on Worg.
All best,
--
Bastien
^ permalink raw reply [flat|nested] 2+ messages in thread
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2014-07-30 21:19 [PATCH] ob-stata.el: new file for stata code evaluation Ista Zahn
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