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 (require 'cl-lib)
  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
  54 (defconst org-babel-header-args:stata
  55   '((width               . :any)
  56     (horizontal          . :any)
  57     (results             . ((file list vector table scalar verbatim)
  58                             (raw org html latex code pp wrap)
  59                             (replace silent append prepend)
  60                             ;; NOTE: not sure 'value' makes sense in stata
  61                             ;; we may want to remove it from the list
  62                             (output value graphics))))
  63   "stata-specific header arguments.")
  64
  65 (add-to-list 'org-babel-tangle-lang-exts '("stata" . "do"))
  66
  67 ;; only ':results output' currently works, so make that the default
  68 (defvar org-babel-default-header-args:stata '((:results . "output")))
  69
  70 (defcustom org-babel-stata-command inferior-STA-program-name
  71   "Name of command to use for executing stata code."
  72   :group 'org-babel
  73   :version "24.4"
  74   :package-version '(Org . "8.3")
  75   :type 'string)
  76
  77 (defvar ess-local-process-name) ; dynamically scoped
  78 (defun org-babel-edit-prep:stata (info)
  79   (let ((session (cdr (assq :session (nth 2 info)))))
  80     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  81       (save-match-data (org-babel-stata-initiate-session session nil)))))
  82
  83 (defun org-babel-expand-body:stata (body params &optional graphics-file)
  84   "Expand BODY according to PARAMS, return the expanded body."
  85   (let ((graphics-file
  86          (or graphics-file (org-babel-stata-graphical-output-file params))))
  87     (mapconcat
  88      #'identity
  89      ((lambda (inside)
  90         (if graphics-file
  91             inside
  92           inside))
  93       (append (org-babel-variable-assignments:stata params)
  94               (list body))) "\n")))
  95
  96 (defun org-babel-execute:stata (body params)
  97   "Execute a block of stata code.
  98 This function is called by `org-babel-execute-src-block'."
  99   (save-excursion
 100     (let* ((result-params (cdr (assq :result-params params)))
 101            (result-type (cdr (assq :result-type params)))
 102            (session (org-babel-stata-initiate-session
 103                      (cdr (assq :session params)) params))
 104            (colnames-p (cdr (assq :colnames params)))
 105            (rownames-p (cdr (assq :rownames params)))
 106            (graphics-file (org-babel-stata-graphical-output-file params))
 107            (full-body (org-babel-expand-body:stata body params graphics-file))
 108            (result
 109             (org-babel-stata-evaluate
 110              session full-body result-type result-params
 111              (or (equal "yes" colnames-p)
 112                  (org-babel-pick-name
 113                   (cdr (assq :colname-names params)) colnames-p))
 114              (or (equal "yes" rownames-p)
 115                  (org-babel-pick-name
 116                   (cdr (assq :rowname-names params)) rownames-p)))))
 117       (if graphics-file nil result))))
 118
 119 (defun org-babel-prep-session:stata (session params)
 120   "Prepare SESSION according to the header arguments specified in PARAMS."
 121   (let* ((session (org-babel-stata-initiate-session session params))
 122          (var-lines (org-babel-variable-assignments:stata params)))
 123     (org-babel-comint-in-buffer session
 124       (mapc (lambda (var)
 125               (end-of-line 1) (insert var) (comint-send-input nil t)
 126               (org-babel-comint-wait-for-output session)) var-lines))
 127     session))
 128
 129 (defun org-babel-load-session:stata (session body params)
 130   "Load BODY into SESSION."
 131   (save-window-excursion
 132     (let ((buffer (org-babel-prep-session:stata session params)))
 133       (with-current-buffer buffer
 134         (goto-char (process-mark (get-buffer-process (current-buffer))))
 135         (insert (org-babel-chomp body)))
 136       buffer)))
 137
 138 ;; helper functions
 139
 140 (defun org-babel-variable-assignments:stata (params)
 141   "Return list of stata statements assigning the block's variables."
 142   (let ((vars (org-babel--get-vars params)))
 143     (mapcar
 144      (lambda (pair)
 145        (org-babel-stata-assign-elisp
 146         (car pair) (cdr pair)
 147         (equal "yes" (cdr (assq :colnames params)))
 148         (equal "yes" (cdr (assq :rownames params)))))
 149      (mapcar
 150       (lambda (i)
 151         (cons (car (nth i vars))
 152               (org-babel-reassemble-table
 153                (cdr (nth i vars))
 154                (cdr (nth i (cdr (assq :colname-names params))))
 155                (cdr (nth i (cdr (assq :rowname-names params)))))))
 156       (org-number-sequence 0 (1- (length vars)))))))
 157
 158 (defun org-babel-stata-quote-csv-field (s)
 159   "Quote field S for export to stata."
 160   (if (stringp s)
 161       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 162     (format "%S" s)))
 163
 164 (defun org-babel-stata-assign-elisp (name value colnames-p rownames-p)
 165   "Construct stata code assigning the elisp VALUE to a variable named NAME."
 166   (if (listp value)
 167       (let ((max (apply #'max (mapcar #'length (cl-remove-if-not
 168                                                 #'sequencep value))))
 169             (min (apply #'min (mapcar #'length (cl-remove-if-not
 170                                                 #'sequencep value))))
 171             (transition-file (org-babel-temp-file "stata-import-")))
 172         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
 173         (unless (listp (car value)) (setq value (list value)))
 174         (with-temp-file transition-file
 175           (insert
 176            (orgtbl-to-csv value '(:fmt org-babel-stata-quote-csv-field))
 177            "\n"))
 178         (let ((file (org-babel-process-file-name transition-file 'noquote))
 179               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 180                           "TRUE" "FALSE"))
 181               (row-names (if rownames-p "1" "NULL")))
 182           (if (= max min)
 183               (format "%s = insheet using \"%s\"" name file)
 184             (format "%s = insheet using \"%s\""
 185                     name file))))
 186     (format "%s = %s" name (org-babel-stata-quote-csv-field value))))
 187
 188 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 189
 190 (defun org-babel-stata-initiate-session (session params)
 191   "If there is not a current stata process then create one."
 192   (unless (string= session "none")
 193     (let ((session (or session "*stata*"))
 194           (ess-ask-for-ess-directory
 195            (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
 196                 (not (cdr (assq :dir params))))))
 197       (if (org-babel-comint-buffer-livep session)
 198           session
 199         (save-window-excursion
 200           (require 'ess) (stata)
 201           (rename-buffer
 202            (if (bufferp session)
 203                (buffer-name session)
 204              (if (stringp session)
 205                  session
 206                (buffer-name))))
 207           (current-buffer))))))
 208
 209 (defun org-babel-stata-associate-session (session)
 210   "Associate stata code buffer with a stata session.
 211 Make SESSION be the inferior ESS process associated with the
 212 current code buffer."
 213   (setq ess-local-process-name
 214         (process-name (get-buffer-process session)))
 215   (ess-make-buffer-current))
 216
 217 (defun org-babel-stata-graphical-output-file (params)
 218   "Name of file to which stata should send graphical output."
 219   (and (member "graphics" (cdr (assq :result-params params)))
 220        (cdr (assq :file params))))
 221
 222 (defvar org-babel-stata-eoe-indicator "display \"org_babel_stata_eoe\"")
 223 (defvar org-babel-stata-eoe-output "org_babel_stata_eoe")
 224
 225 (defvar org-babel-stata-write-object-command "outsheet using \"%s\"")
 226
 227 (defun org-babel-stata-evaluate
 228   (session body result-type result-params column-names-p row-names-p)
 229   "Evaluate stata code in BODY."
 230   (if session
 231       (org-babel-stata-evaluate-session
 232        session body result-type result-params column-names-p row-names-p)
 233     (org-babel-stata-evaluate-external-process
 234      body result-type result-params column-names-p row-names-p)))
 235
 236 (defun org-babel-stata-evaluate-external-process
 237   (body result-type result-params column-names-p row-names-p)
 238   "Evaluate BODY in external stata process.
 239 If RESULT-TYPE equals 'output then return standard output as a
 240 string.  If RESULT-TYPE equals 'value then return the value of the
 241 last statement in BODY, as elisp."
 242   (cl-case result-type
 243     (value
 244      (let ((tmp-file (org-babel-temp-file "stata-")))
 245        (org-babel-eval org-babel-stata-command
 246                        (format org-babel-stata-write-object-command
 247                                (org-babel-process-file-name tmp-file 'noquote)
 248                                (format "begin\n%s\nend" body)))
 249        (org-babel-stata-process-value-result
 250         (org-babel-result-cond result-params
 251           (with-temp-buffer
 252             (insert-file-contents tmp-file)
 253             (buffer-string))
 254           (org-babel-import-elisp-from-file tmp-file '(4)))
 255         column-names-p)))
 256     (output (org-babel-eval org-babel-stata-command body))))
 257
 258 (defun org-babel-stata-evaluate-session
 259   (session body result-type result-params column-names-p row-names-p)
 260   "Evaluate BODY in SESSION.
 261 If RESULT-TYPE equals 'output then return standard output as a
 262 string.  If RESULT-TYPE equals 'value then return the value of the
 263 last statement in BODY, as elisp."
 264   (cl-case result-type
 265     (value
 266      (with-temp-buffer
 267        (insert (org-babel-chomp body))
 268        (let ((ess-local-process-name
 269               (process-name (get-buffer-process session)))
 270              (ess-eval-visibly-p nil))
 271          (ess-eval-buffer nil)))
 272      (let ((tmp-file (org-babel-temp-file "stata-")))
 273        (org-babel-comint-eval-invisibly-and-wait-for-file
 274         session tmp-file
 275         (format org-babel-stata-write-object-command
 276                 (org-babel-process-file-name tmp-file 'noquote) "ans"))
 277        (org-babel-stata-process-value-result
 278         (org-babel-result-cond result-params
 279           (with-temp-buffer
 280             (insert-file-contents tmp-file)
 281             (buffer-string))
 282           (org-babel-import-elisp-from-file tmp-file '(4)))
 283         column-names-p)))
 284     (output
 285      (mapconcat
 286       #'org-babel-chomp
 287       (butlast
 288        (delq nil
 289              (mapcar
 290               (lambda (line) (when (> (length line) 0) line))
 291               (mapcar
 292                (lambda (line) ;; cleanup extra prompts left in output
 293                  (if (string-match
 294                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 295                      (substring line (match-end 1))
 296                    line))
 297                (org-babel-comint-with-output (session org-babel-stata-eoe-output)
 298                  (insert (mapconcat #'org-babel-chomp
 299                                     (list body org-babel-stata-eoe-indicator)
 300                                     "\n"))
 301                  (inferior-ess-send-input)))))) "\n"))))
 302
 303 (defun org-babel-stata-process-value-result (result column-names-p)
 304   "stata-specific processing of return value.
 305 Insert hline if column names in output have been requested."
 306   (if column-names-p
 307       (cons (car result) (cons 'hline (cdr result)))
 308     result))
 309
 310 (provide 'ob-stata)
 311
 312 ;;; ob-stata.el ends here