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.
This commit is contained in:
Ista Zahn
Bastien Guerry
parent
350fdfd676
commit
7326d10dc5
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
Loading…
Reference in New Issue