;;; ob-sql.el --- org-babel functions for sql evaluation
-;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research
;;
;; Also SQL evaluation generally takes place inside of a database.
;;
-;; For now lets just allow a generic ':cmdline' header argument.
+;; Header args used:
+;; - engine
+;; - cmdline
+;; - dbhost
+;; - dbuser
+;; - dbpassword
+;; - database
+;; - colnames (default, nil, means "yes")
+;; - result-params
+;; - out-file
+;; The following are used but not really implemented for SQL:
+;; - colname-names
+;; - rownames
+;; - rowname-names
;;
;; TODO:
;;
;; - support for sessions
-;; - add more useful header arguments (user, passwd, database, etc...)
;; - support for more engines (currently only supports mysql)
;; - what's a reasonable way to drop table data into SQL?
;;
(eval-when-compile (require 'cl))
(declare-function org-table-import "org-table" (file arg))
-(declare-function orgtbl-to-csv "org-table" (TABLE PARAMS))
+(declare-function orgtbl-to-csv "org-table" (table params))
+(declare-function org-table-to-lisp "org-table" (&optional txt))
(defvar org-babel-default-header-args:sql '())
-(defvar org-babel-header-args:sql
- '((engine . :any)
- (out-file . :any)))
+(defconst org-babel-header-args:sql
+ '((engine . :any)
+ (out-file . :any)
+ (dbhost . :any)
+ (dbuser . :any)
+ (dbpassword . :any)
+ (database . :any))
+ "SQL-specific header arguments.")
(defun org-babel-expand-body:sql (body params)
"Expand BODY according to the values of PARAMS."
(org-babel-sql-expand-vars
body (mapcar #'cdr (org-babel-get-header params :var))))
+(defun dbstring-mysql (host user password database)
+ "Make MySQL cmd line args for database connection. Pass nil to omit that arg."
+ (combine-and-quote-strings
+ (remq nil
+ (list (when host (concat "-h" host))
+ (when user (concat "-u" user))
+ (when password (concat "-p" password))
+ (when database (concat "-D" database))))))
+
(defun org-babel-execute:sql (body params)
"Execute a block of Sql code with Babel.
This function is called by `org-babel-execute-src-block'."
(let* ((result-params (cdr (assoc :result-params params)))
(cmdline (cdr (assoc :cmdline params)))
+ (dbhost (cdr (assoc :dbhost params)))
+ (dbuser (cdr (assoc :dbuser params)))
+ (dbpassword (cdr (assoc :dbpassword params)))
+ (database (cdr (assoc :database params)))
(engine (cdr (assoc :engine params)))
+ (colnames-p (not (equal "no" (cdr (assoc :colnames params)))))
(in-file (org-babel-temp-file "sql-in-"))
(out-file (or (cdr (assoc :out-file params))
(org-babel-temp-file "sql-out-")))
(header-delim "")
(command (case (intern engine)
- ('dbi (format "dbish --batch '%s' < %s | sed '%s' > %s"
+ ('dbi (format "dbish --batch %s < %s | sed '%s' > %s"
(or cmdline "")
(org-babel-process-file-name in-file)
- "/^+/d;s/^\|//;$d"
+ "/^+/d;s/^|//;s/(NULL)/ /g;$d"
(org-babel-process-file-name out-file)))
('monetdb (format "mclient -f tab %s < %s > %s"
(or cmdline "")
(or cmdline "")
(org-babel-process-file-name in-file)
(org-babel-process-file-name out-file)))
- ('mysql (format "mysql %s < %s > %s"
+ ('mysql (format "mysql %s %s %s < %s > %s"
+ (dbstring-mysql dbhost dbuser dbpassword database)
+ (if colnames-p "" "-N")
(or cmdline "")
(org-babel-process-file-name in-file)
(org-babel-process-file-name out-file)))
(t ""))
(org-babel-expand-body:sql body params)))
(message command)
- (shell-command command)
- (if (or (member "scalar" result-params)
- (member "verbatim" result-params)
- (member "html" result-params)
- (member "code" result-params)
- (equal (point-min) (point-max)))
- (with-temp-buffer
+ (org-babel-eval command "")
+ (org-babel-result-cond result-params
+ (with-temp-buffer
(progn (insert-file-contents-literally out-file) (buffer-string)))
(with-temp-buffer
- ;; need to figure out what the delimiter is for the header row
- (with-temp-buffer
- (insert-file-contents out-file)
- (goto-char (point-min))
- (when (re-search-forward "^\\(-+\\)[^-]" nil t)
- (setq header-delim (match-string-no-properties 1)))
- (goto-char (point-max))
- (forward-char -1)
- (while (looking-at "\n")
- (delete-char 1)
- (goto-char (point-max))
- (forward-char -1))
- (write-file out-file))
+ (cond
+ ((or (eq (intern engine) 'mysql)
+ (eq (intern engine) 'dbi)
+ (eq (intern engine) 'postgresql))
+ ;; Add header row delimiter after column-names header in first line
+ (cond
+ (colnames-p
+ (with-temp-buffer
+ (insert-file-contents out-file)
+ (goto-char (point-min))
+ (forward-line 1)
+ (insert "-\n")
+ (setq header-delim "-")
+ (write-file out-file)))))
+ (t
+ ;; Need to figure out the delimiter for the header row
+ (with-temp-buffer
+ (insert-file-contents out-file)
+ (goto-char (point-min))
+ (when (re-search-forward "^\\(-+\\)[^-]" nil t)
+ (setq header-delim (match-string-no-properties 1)))
+ (goto-char (point-max))
+ (forward-char -1)
+ (while (looking-at "\n")
+ (delete-char 1)
+ (goto-char (point-max))
+ (forward-char -1))
+ (write-file out-file))))
(org-table-import out-file '(16))
(org-babel-reassemble-table
(mapcar (lambda (x)
(lambda (pair)
(setq body
(replace-regexp-in-string
- (format "\$%s" (car pair))
- ((lambda (val)
- (if (listp val)
- ((lambda (data-file)
- (with-temp-file data-file
- (insert (orgtbl-to-csv
- val '(:fmt (lambda (el) (if (stringp el)
- el
- (format "%S" el)))))))
- data-file)
- (org-babel-temp-file "sql-data-"))
- (if (stringp val) val (format "%S" val))))
- (cdr pair))
+ (format "$%s" (car pair))
+ (let ((val (cdr pair)))
+ (if (listp val)
+ (let ((data-file (org-babel-temp-file "sql-data-")))
+ (with-temp-file data-file
+ (insert (orgtbl-to-csv
+ val '(:fmt (lambda (el) (if (stringp el)
+ el
+ (format "%S" el)))))))
+ data-file)
+ (if (stringp val) val (format "%S" val))))
body)))
vars)
body)