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@izahn izahn/ob-stata.el
Last active Aug 29, 2015

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Preliminary Stata support for org-babel in emacs
;;; ob-stata.el --- org-babel functions for stata code evaluation
;; Copyright (C) 2014 Ista Zahn
;; Author: Ista Zahn, based on ob-julia.el by G. Jay Kerns, and ob-R.el
;; by Eric Schulte and 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".
;;; 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)
(output value graphics))))
"stata-specific header arguments.")
(add-to-list 'org-babel-tangle-lang-exts '("stata" . "do"))
(defvar org-babel-default-header-args:stata '())
(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 . "8.0")
: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\"")
;; The following was a very complicated write object command
;; The replacement needs to add error catching
;(defvar org-babel-stata-write-object-command "{function(object,transfer.file){object;invisible(if(inherits(try({tfile<-tempfile();write.table(object,file=tfile,sep=\"\\t\",na=\"nil\",row.names=%s,col.names=%s,quote=FALSE);file.rename(tfile,transfer.file)},silent=TRUE),\"try-error\")){if(!file.exists(transfer.file))file.create(transfer.file)})}}(object=%s,transfer.file=\"%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
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