contrib/lisp/ob-stata.el

   1 ;;; ob-stata.el --- org-babel functions for stata code evaluation
   2
   3 ;; Copyright (C) 2014 Ista Zahn
   4 ;; Author: Ista Zahn istazahn@gmail.com
   5 ;;      G. Jay Kerns
   6 ;;      Eric Schulte
   7 ;;      Dan Davison
   8
   9
  10 ;; This file is not part of GNU Emacs.
  11
  12 ;; This program is free software; you can redistribute it and/or modify
  13 ;; it under the terms of the GNU General Public License as published by
  14 ;; the Free Software Foundation; either version 3, or (at your option)
  15 ;; any later version.
  16 ;;
  17 ;; This program is distributed in the hope that it will be useful,
  18 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;; GNU General Public License for more details.
  21 ;;
  22 ;; You should have received a copy of the GNU General Public License
  23 ;; along with GNU Emacs; see the file COPYING.  If not, write to the
  24 ;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
  25 ;; Boston, MA 02110-1301, USA.
  26
  27 ;;; Commentary:
  28
  29 ;; The file provides Org-Babel support for evaluating stata code.
  30 ;; It is basically result of find-and-replace "stata" for "julia"
  31 ;; in ob-julia.el by G. Jay Kerns. Only ":results output" works: the
  32 ;; header args must include ":results output" (this is the default).
  33 ;; Note that I'm not sure ':results value' makes sense or is useful
  34 ;; but I have left all the value-processing stuff inherited from
  35 ;; ob-julia and ob-R. ':results graphics' would be nice, but I have
  36 ;; not tried to implement it.
  37 ;; --Ista, 07/30/2014
  38
  39 ;;; Requirements:
  40 ;; Stata: http://stata.com
  41 ;; ESS: http://ess.r-project.org
  42
  43 ;;; Code:
  44 (require 'ob)
  45 (eval-when-compile (require 'cl))
  46
  47 (declare-function orgtbl-to-csv "org-table" (table params))
  48 (declare-function stata "ext:ess-stata" (&optional start-args))
  49 (declare-function inferior-ess-send-input "ext:ess-inf" ())
  50 (declare-function ess-make-buffer-current "ext:ess-inf" ())
  51 (declare-function ess-eval-buffer "ext:ess-inf" (vis))
  52 (declare-function org-number-sequence "org-compat" (from &optional to inc))
  53 (declare-function org-remove-if-not "org" (predicate seq))
  54
  55 (defconst org-babel-header-args:stata
  56   '((width               . :any)
  57     (horizontal          . :any)
  58     (results             . ((file list vector table scalar verbatim)
  59                             (raw org html latex code pp wrap)
  60                             (replace silent append prepend)
  61                             ;; NOTE: not sure 'value' makes sense in stata
  62                             ;; we may want to remove it from the list
  63                             (output value graphics))))
  64   "stata-specific header arguments.")
  65
  66 (add-to-list 'org-babel-tangle-lang-exts '("stata" . "do"))
  67
  68 ;; only ':results output' currently works, so make that the default
  69 (defvar org-babel-default-header-args:stata '((:results . "output")))
  70
  71 (defcustom org-babel-stata-command inferior-STA-program-name
  72   "Name of command to use for executing stata code."
  73   :group 'org-babel
  74   :version "24.4"
  75   :package-version '(Org . "8.3")
  76   :type 'string)
  77
  78 (defvar ess-local-process-name) ; dynamically scoped
  79 (defun org-babel-edit-prep:stata (info)
  80   (let ((session (cdr (assoc :session (nth 2 info)))))
  81     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  82       (save-match-data (org-babel-stata-initiate-session session nil)))))
  83
  84 (defun org-babel-expand-body:stata (body params &optional graphics-file)
  85   "Expand BODY according to PARAMS, return the expanded body."
  86   (let ((graphics-file
  87          (or graphics-file (org-babel-stata-graphical-output-file params))))
  88     (mapconcat
  89      #'identity
  90      ((lambda (inside)
  91         (if graphics-file
  92             inside
  93           inside))
  94       (append (org-babel-variable-assignments:stata params)
  95               (list body))) "\n")))
  96
  97 (defun org-babel-execute:stata (body params)
  98   "Execute a block of stata code.
  99 This function is called by `org-babel-execute-src-block'."
 100   (save-excursion
 101     (let* ((result-params (cdr (assoc :result-params params)))
 102            (result-type (cdr (assoc :result-type params)))
 103            (session (org-babel-stata-initiate-session
 104                      (cdr (assoc :session params)) params))
 105            (colnames-p (cdr (assoc :colnames params)))
 106            (rownames-p (cdr (assoc :rownames params)))
 107            (graphics-file (org-babel-stata-graphical-output-file params))
 108            (full-body (org-babel-expand-body:stata body params graphics-file))
 109            (result
 110             (org-babel-stata-evaluate
 111              session full-body result-type result-params
 112              (or (equal "yes" colnames-p)
 113                  (org-babel-pick-name
 114                   (cdr (assoc :colname-names params)) colnames-p))
 115              (or (equal "yes" rownames-p)
 116                  (org-babel-pick-name
 117                   (cdr (assoc :rowname-names params)) rownames-p)))))
 118       (if graphics-file nil result))))
 119
 120 (defun org-babel-prep-session:stata (session params)
 121   "Prepare SESSION according to the header arguments specified in PARAMS."
 122   (let* ((session (org-babel-stata-initiate-session session params))
 123          (var-lines (org-babel-variable-assignments:stata params)))
 124     (org-babel-comint-in-buffer session
 125       (mapc (lambda (var)
 126               (end-of-line 1) (insert var) (comint-send-input nil t)
 127               (org-babel-comint-wait-for-output session)) var-lines))
 128     session))
 129
 130 (defun org-babel-load-session:stata (session body params)
 131   "Load BODY into SESSION."
 132   (save-window-excursion
 133     (let ((buffer (org-babel-prep-session:stata session params)))
 134       (with-current-buffer buffer
 135         (goto-char (process-mark (get-buffer-process (current-buffer))))
 136         (insert (org-babel-chomp body)))
 137       buffer)))
 138
 139 ;; helper functions
 140
 141 (defun org-babel-variable-assignments:stata (params)
 142   "Return list of stata statements assigning the block's variables."
 143   (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
 144     (mapcar
 145      (lambda (pair)
 146        (org-babel-stata-assign-elisp
 147         (car pair) (cdr pair)
 148         (equal "yes" (cdr (assoc :colnames params)))
 149         (equal "yes" (cdr (assoc :rownames params)))))
 150      (mapcar
 151       (lambda (i)
 152         (cons (car (nth i vars))
 153               (org-babel-reassemble-table
 154                (cdr (nth i vars))
 155                (cdr (nth i (cdr (assoc :colname-names params))))
 156                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 157       (org-number-sequence 0 (1- (length vars)))))))
 158
 159 (defun org-babel-stata-quote-csv-field (s)
 160   "Quote field S for export to stata."
 161   (if (stringp s)
 162       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 163     (format "%S" s)))
 164
 165 (defun org-babel-stata-assign-elisp (name value colnames-p rownames-p)
 166   "Construct stata code assigning the elisp VALUE to a variable named NAME."
 167   (if (listp value)
 168       (let ((max (apply #'max (mapcar #'length (org-remove-if-not
 169                                                 #'sequencep value))))
 170             (min (apply #'min (mapcar #'length (org-remove-if-not
 171                                                 #'sequencep value))))
 172             (transition-file (org-babel-temp-file "stata-import-")))
 173         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 174         (unless (listp (car value)) (setq value (list value)))
 175         (with-temp-file transition-file
 176           (insert
 177            (orgtbl-to-csv value '(:fmt org-babel-stata-quote-csv-field))
 178            "\n"))
 179         (let ((file (org-babel-process-file-name transition-file 'noquote))
 180               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 181                           "TRUE" "FALSE"))
 182               (row-names (if rownames-p "1" "NULL")))
 183           (if (= max min)
 184               (format "%s = insheet using \"%s\"" name file)
 185             (format "%s = insheet using \"%s\""
 186                     name file))))
 187     (format "%s = %s" name (org-babel-stata-quote-csv-field value))))
 188
 189 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 190
 191 (defun org-babel-stata-initiate-session (session params)
 192   "If there is not a current stata process then create one."
 193   (unless (string= session "none")
 194     (let ((session (or session "*stata*"))
 195           (ess-ask-for-ess-directory
 196            (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
 197                 (not (cdr (assoc :dir params))))))
 198       (if (org-babel-comint-buffer-livep session)
 199           session
 200         (save-window-excursion
 201           (require 'ess) (stata)
 202           (rename-buffer
 203            (if (bufferp session)
 204                (buffer-name session)
 205              (if (stringp session)
 206                  session
 207                (buffer-name))))
 208           (current-buffer))))))
 209
 210 (defun org-babel-stata-associate-session (session)
 211   "Associate stata code buffer with a stata session.
 212 Make SESSION be the inferior ESS process associated with the
 213 current code buffer."
 214   (setq ess-local-process-name
 215         (process-name (get-buffer-process session)))
 216   (ess-make-buffer-current))
 217
 218 (defun org-babel-stata-graphical-output-file (params)
 219   "Name of file to which stata should send graphical output."
 220   (and (member "graphics" (cdr (assq :result-params params)))
 221        (cdr (assq :file params))))
 222
 223 (defvar org-babel-stata-eoe-indicator "display \"org_babel_stata_eoe\"")
 224 (defvar org-babel-stata-eoe-output "org_babel_stata_eoe")
 225
 226 (defvar org-babel-stata-write-object-command "outsheet using \"%s\"")
 227
 228 (defun org-babel-stata-evaluate
 229   (session body result-type result-params column-names-p row-names-p)
 230   "Evaluate stata code in BODY."
 231   (if session
 232       (org-babel-stata-evaluate-session
 233        session body result-type result-params column-names-p row-names-p)
 234     (org-babel-stata-evaluate-external-process
 235      body result-type result-params column-names-p row-names-p)))
 236
 237 (defun org-babel-stata-evaluate-external-process
 238   (body result-type result-params column-names-p row-names-p)
 239   "Evaluate BODY in external stata process.
 240 If RESULT-TYPE equals 'output then return standard output as a
 241 string.  If RESULT-TYPE equals 'value then return the value of the
 242 last statement in BODY, as elisp."
 243   (case result-type
 244     (value
 245      (let ((tmp-file (org-babel-temp-file "stata-")))
 246        (org-babel-eval org-babel-stata-command
 247                        (format org-babel-stata-write-object-command
 248                                (org-babel-process-file-name tmp-file 'noquote)
 249                                (format "begin\n%s\nend" body)))
 250        (org-babel-stata-process-value-result
 251         (org-babel-result-cond result-params
 252           (with-temp-buffer
 253             (insert-file-contents tmp-file)
 254             (buffer-string))
 255           (org-babel-import-elisp-from-file tmp-file '(4)))
 256         column-names-p)))
 257     (output (org-babel-eval org-babel-stata-command body))))
 258
 259 (defun org-babel-stata-evaluate-session
 260   (session body result-type result-params column-names-p row-names-p)
 261   "Evaluate BODY in SESSION.
 262 If RESULT-TYPE equals 'output then return standard output as a
 263 string.  If RESULT-TYPE equals 'value then return the value of the
 264 last statement in BODY, as elisp."
 265   (case result-type
 266     (value
 267      (with-temp-buffer
 268        (insert (org-babel-chomp body))
 269        (let ((ess-local-process-name
 270               (process-name (get-buffer-process session)))
 271              (ess-eval-visibly-p nil))
 272          (ess-eval-buffer nil)))
 273      (let ((tmp-file (org-babel-temp-file "stata-")))
 274        (org-babel-comint-eval-invisibly-and-wait-for-file
 275         session tmp-file
 276         (format org-babel-stata-write-object-command
 277                 (org-babel-process-file-name tmp-file 'noquote) "ans"))
 278        (org-babel-stata-process-value-result
 279         (org-babel-result-cond result-params
 280           (with-temp-buffer
 281             (insert-file-contents tmp-file)
 282             (buffer-string))
 283           (org-babel-import-elisp-from-file tmp-file '(4)))
 284         column-names-p)))
 285     (output
 286      (mapconcat
 287       #'org-babel-chomp
 288       (butlast
 289        (delq nil
 290              (mapcar
 291               (lambda (line) (when (> (length line) 0) line))
 292               (mapcar
 293                (lambda (line) ;; cleanup extra prompts left in output
 294                  (if (string-match
 295                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 296                      (substring line (match-end 1))
 297                    line))
 298                (org-babel-comint-with-output (session org-babel-stata-eoe-output)
 299                  (insert (mapconcat #'org-babel-chomp
 300                                     (list body org-babel-stata-eoe-indicator)
 301                                     "\n"))
 302                  (inferior-ess-send-input)))))) "\n"))))
 303
 304 (defun org-babel-stata-process-value-result (result column-names-p)
 305   "stata-specific processing of return value.
 306 Insert hline if column names in output have been requested."
 307   (if column-names-p
 308       (cons (car result) (cons 'hline (cdr result)))
 309     result))
 310
 311 (provide 'ob-stata)
 312
 313 ;;; ob-stata.el ends here