org-mode/contrib/babel/library-of-babel.org

The Library of Babel

• Introduction
• Simple
• File I/O
  • Reading and writing files
  • Remote files
    • json
    • Google docs
      • Read a document from Google docs
      • Write a document to a Google docs
• Plotting code
  • R
  • Gnuplot
• Org reference
  • Headline references
• Tables
  • LaTeX Table Export
    • booktabs
    • longtable
    • booktabs-notes
  • Elegant lisp for transposing a matrix.
  • Convert every element of a table to a string
• Misc
  • File-specific Version Control logging
  • Trivial python code blocks
  • Arithmetic
• GANTT Charts
• Available languages
  • From Org's core
  • From Org's contrib/babel/langs

Introduction

The Library of Babel is an extensible collection of ready-made and easily-shortcut-callable source-code blocks for handling common tasks. Org-babel comes pre-populated with the source-code blocks located in this file. It is possible to add source-code blocks from any org-mode file to the library by calling (org-babel-lob-ingest "path/to/file.org").

This file is included in worg mainly less for viewing through the web interface, and more for contribution through the worg git repository. If you have code snippets that you think others may find useful please add them to this file and contribute them to worg.

The raw Org-mode text of this file can be downloaded at library-of-babel.org

Simple

A collection of simple utility functions:

  input

File I/O

Reading and writing files

Read the contents of the file at file. The :results vector and :results scalar header arguments can be used to read the contents of file as either a table or a string.

  (if (string= format "csv")
      (with-temp-buffer
        (org-table-import (expand-file-name file) nil)
        (org-table-to-lisp))
    (with-temp-buffer
      (insert-file-contents (expand-file-name file))
      (buffer-string)))

Write data to a file at file. If data is a list, then write it as a table in traditional Org-mode table syntax.

  (flet ((echo (r) (if (stringp r) r (format "%S" r))))
    (with-temp-file file
      (case (and (listp data)
                 (or ext (intern (file-name-extension file))))
        ('tsv (insert (orgtbl-to-tsv data '(:fmt echo))))
        ('csv (insert (orgtbl-to-csv data '(:fmt echo))))
        (t    (org-babel-insert-result data)))))
  nil

Remote files

json

Read local or remote file in json format into emacs-lisp objects.

  (require 'json)
  (cond
   (file
    (with-temp-filebuffer file
      (goto-char (point-min))
      (json-read)))
   (url
    (require 'w3m)
    (with-temp-buffer
      (w3m-retrieve url)
      (goto-char (point-min))
      (json-read))))

Google docs

The following code blocks make use of the googlecl Google command line tool. This tool provides functionality for accessing Google services from the command line, and the following code blocks use googlecl for reading from and writing to Google docs with Org-mode code blocks.

Read a document from Google docs

The google command seems to be throwing "Moved Temporarily" errors when trying to download textual documents, but this is working fine for spreadsheets.

  (let* ((file (concat title "." format))
         (cmd (format "google docs get --format %S --title %S" format title)))
    (message cmd) (message (shell-command-to-string cmd))
    (prog1 (if (string= format "csv")
               (with-temp-buffer
                 (org-table-import (shell-quote-argument file) '(4))
                 (org-table-to-lisp))
             (with-temp-buffer
               (insert-file-contents (shell-quote-argument file))
               (buffer-string)))
      (delete-file file)))

For example, a line like the following can be used to read the contents of a spreadsheet named num-cells into a table.

#+call: gdoc-read(title="num-cells"")

A line like the following can be used to read the contents of a document as a string.

#+call: gdoc-read(title="loremi", :format "txt")

Write a document to a Google docs

Write data to a google document named title. If data is tabular it will be saved to a spreadsheet, otherwise it will be saved as a normal document.

  (let* ((format (if (listp data) "csv" "txt"))
         (tmp-file (make-temp-file "org-babel-google-doc" nil (concat "." format)))
         (cmd (format "google docs upload --title %S %S" title tmp-file)))
    (with-temp-file tmp-file
      (insert
       (if (listp data)
           (orgtbl-to-csv
            data '(:fmt (lambda (el) (if (stringp el) el (format "%S" el)))))
         (if (stringp data) data (format "%S" data)))))
    (message cmd)
    (prog1 (shell-command-to-string cmd) (delete-file tmp-file)))

example usage

#+source: fibs
#+begin_src emacs-lisp :var n=8
  (flet ((fib (m) (if (< m 2) 1 (+ (fib (- m 1)) (fib (- m 2))))))
    (mapcar (lambda (el) (list el (fib el))) (number-sequence 0 (- n 1))))
#+end_src

#+call: gdoc-write(title="fibs", data=fibs(n=10))

Plotting code

R

Plot column 2 (y axis) against column 1 (x axis). Columns 3 and beyond, if present, are ignored.

plot(data)

1	2
2	4
3	9
4	16
5	25

nil

Gnuplot

Org reference

Headline references

  (save-excursion
    (when file (get-file-buffer file))
    (org-open-link-from-string (org-make-link-string headline))
    (save-restriction
      (org-narrow-to-subtree)
      (buffer-string)))

Tables

LaTeX Table Export

booktabs

This source block can be used to wrap a table in the latex booktabs environment. The source block adds a toprule and bottomrule (so don't use hline at the top or bottom of the table). The hline after the header is replaced with a midrule.

Note that this function bypasses the Org-mode LaTeX exporter and calls orgtbl-to-generic to create the output table. This means that the entries in the table are not translated from Org-mode to LaTeX.

It takes the following arguments – all but the first two are optional.

arg	description
table	a reference to the table
align	alignment string
env	optional environment, default to "tabular"
width	optional width specification string

  (flet ((to-tab (tab)
                 (orgtbl-to-generic
                  (mapcar (lambda (lis)
                            (if (listp lis)
                                (mapcar (lambda (el)
                                          (if (stringp el)
                                              el
                                            (format "%S" el))) lis)
                              lis)) tab)
                  (list :lend " \\\\" :sep " & " :hline "\\hline"))))
    (org-fill-template
     "
  \\begin{%env}%width%align
  \\toprule
  %table
  \\bottomrule
  \\end{%env}\n"
     (list
      (cons "env"       (or env "table"))
      (cons "width"     (if width (format "{%s}" width) ""))
      (cons "align"     (if align (format "{%s}" align) ""))
      (cons "table"
            ;; only use \midrule if it looks like there are column headers
            (if (equal 'hline (second table))
                (concat (to-tab (list (first table)))
                        "\n\\midrule\n"
                        (to-tab (cddr table)))
              (to-tab table))))))

longtable

This block can be used to wrap a table in the latex longtable environment, it takes the following arguments – all but the first two are optional.

arg	description
table	a reference to the table
align	optional alignment string
width	optional width specification string
hline	the string to use as hline separator, defaults to "\\hline"
head	optional "head" string
firsthead	optional "firsthead" string
foot	optional "foot" string
lastfoot	optional "lastfoot" string

  (org-fill-template
   "
  \\begin{longtable}%width%align
  %firsthead
  %head
  %foot
  %lastfoot
  
  %table
  \\end{longtable}\n"
   (list
    (cons "width"     (if width (format "{%s}" width) ""))
    (cons "align"     (if align (format "{%s}" align) ""))
    (cons "firsthead" (if firsthead (concat firsthead "\n\\endfirsthead\n") ""))
    (cons "head"      (if head (concat head "\n\\endhead\n") ""))
    (cons "foot"      (if foot (concat foot "\n\\endfoot\n") ""))
    (cons "lastfoot"  (if lastfoot (concat lastfoot "\n\\endlastfoot\n") ""))
    (cons "table" (orgtbl-to-generic
                   (mapcar (lambda (lis)
                             (if (listp lis)
                                 (mapcar (lambda (el)
                                           (if (stringp el)
                                               el
                                             (format "%S" el))) lis)
                               lis)) table)
                   (list :lend " \\\\" :sep " & " :hline hline)))))

booktabs-notes

This source block builds on /tec/org-mode/src/commit/7e93b90f8816346a16ad49cee22870b17c05b211/contrib/babel/booktabs. It accepts two additional arguments, both of which are optional.

arg	description
notes	an org-mode table with footnotes
lspace	if non-nil, insert addlinespace after bottomrule

An example footnote to the arguments table specifies the column span. Note the use of LaTeX, rather than Org-mode, markup.

μlticolumn{2}{l}{This is a footnote to the \emph{arguments} table.}

  (flet ((to-tab (tab)
                 (orgtbl-to-generic
                  (mapcar (lambda (lis)
                            (if (listp lis)
                                (mapcar (lambda (el)
                                          (if (stringp el)
                                              el
                                            (format "%S" el))) lis)
                              lis)) tab)
                  (list :lend " \\\\" :sep " & " :hline "\\hline"))))
    (org-fill-template
     "
    \\begin{%env}%width%align
    \\toprule
    %table
    \\bottomrule%spacer
    %notes
    \\end{%env}\n"
     (list
      (cons "env"       (or env "table"))
      (cons "width"     (if width (format "{%s}" width) ""))
      (cons "align"     (if align (format "{%s}" align) ""))
      (cons "spacer"    (if lspace "\\addlinespace" ""))
      (cons "table"
            ;; only use \midrule if it looks like there are column headers
            (if (equal 'hline (second table))
                (concat (to-tab (list (first table)))
                        "\n\\midrule\n"
                        (to-tab (cddr table)))
              (to-tab table)))
      (cons "notes" (if notes (to-tab notes) ""))
      )))

Elegant lisp for transposing a matrix.

1	2	3
4	5	6

  (apply #'mapcar* #'list table)

1	4
2	5
3	6

Convert every element of a table to a string

1	2	3
a	b	c

  (defun all-to-string (tbl)
    (if (listp tbl)
        (mapcar #'all-to-string tbl)
      (if (stringp tbl)
          tbl
        (format "%s" tbl))))
  (all-to-string tbl)

  (mapcar (lambda (row) (mapcar (lambda (cell) (stringp cell)) row)) tbl)

nil	nil	nil
t	t	t

  (mapcar (lambda (row) (mapcar (lambda (cell) (stringp cell)) row)) tbl)

t	t	t
t	t	t

Misc

File-specific Version Control logging

This function will attempt to retrieve the entire commit log for the file associated with the current buffer and insert this log into the export. The function uses the Emacs VC commands to interface to the local version control system, but has only been tested to work with Git. 'limit' is currently unsupported.

  ;; Most of this code is copied from vc.el vc-print-log
  (require 'vc)
  (when (vc-find-backend-function
         (vc-backend (buffer-file-name (get-buffer buf))) 'print-log)
    (let ((limit -1)
          (vc-fileset nil)
          (backend nil)
          (files nil))
      (with-current-buffer (get-buffer buf)
        (setq vc-fileset (vc-deduce-fileset t)) ; FIXME: Why t? --Stef
        (setq backend (car vc-fileset))
        (setq files (cadr vc-fileset)))
      (with-temp-buffer 
        (let ((status (vc-call-backend
                       backend 'print-log files (current-buffer))))
          (when (and (processp status)   ; Make sure status is a process
                     (= 0 (process-exit-status status))) ; which has not terminated
            (while (not (eq 'exit (process-status status)))
              (sit-for 1 t)))
          (buffer-string)))))

Trivial python code blocks

a

a + b

Arithmetic

  (+ a b)

  (- a b)

  (* a b)

  (/ a b)

GANTT Charts

The elispgantt source block was sent to the mailing list by Eric Fraga. It was modified slightly by Tom Dye.

  (let ((dates "")
        (entries (nthcdr 2 table))
        (milestones "")
        (nmilestones 0)
        (ntasks 0)
        (projecttime 0)
        (tasks "")
        (xlength 1))
    (message "Initial: %s\n" table)
    (message "Entries: %s\n" entries)
    (while entries
      (let ((entry (first entries)))
        (if (listp entry)
            (let ((id (first entry))
                  (type (nth 1 entry))
                  (label (nth 2 entry))
                  (task (nth 3 entry))
                  (dependencies (nth 4 entry))
                  (start (nth 5 entry))
                  (duration (nth 6 entry))
                  (end (nth 7 entry))
                  (alignment (nth 8 entry)))
              (if (> start projecttime) (setq projecttime start))
              (if (string= type "task")
                  (let ((end (+ start duration))
                        (textposition (+ start (/ duration 2)))
                        (flush ""))
                    (if (string= alignment "left")
                        (progn
                          (setq textposition start)
                          (setq flush "[left]"))
                      (if (string= alignment "right")
                          (progn
                            (setq textposition end)
                            (setq flush "[right]"))))
                    (setq tasks
                          (format "%s  \\gantttask{%s}{%s}{%d}{%d}{%d}{%s}\n"
                                  tasks label task start end textposition flush))
                    (setq ntasks (+ 1 ntasks))
                    (if (> end projecttime)
                        (setq projecttime end)))
                (if (string= type "milestone")
                    (progn
                      (setq milestones
                            (format
                             "%s  \\ganttmilestone{$\\begin{array}{c}\\mbox{%s}\\\\ \\mbox{%s}\\end{array}$}{%d}\n"
                             milestones label task start))
                      (setq nmilestones (+ 1 nmilestones)))
                  (if (string= type "date")
                      (setq dates (format "%s  \\ganttdateline{%s}{%d}\n"
                                          dates label start))
                    (message "Ignoring entry with type %s\n" type)))))
          (message "Ignoring non-list entry %s\n" entry)) ; end if list entry
        (setq entries (cdr entries))))  ; end while entries left
    (format "\\pgfdeclarelayer{background}
  \\pgfdeclarelayer{foreground}
  \\pgfsetlayers{background,foreground}
  \\renewcommand{\\ganttprojecttime}{%d}
  \\renewcommand{\\ganttntasks}{%d}
  \\noindent
  \\begin{tikzpicture}[y=-0.75cm,x=0.75\\textwidth]
    \\begin{pgfonlayer}{background}
      \\draw[very thin, red!10!white] (0,1+\\ganttntasks) grid [ystep=0.75cm,xstep=1/\\ganttprojecttime] (1,0);
      \\draw[\\ganttdatelinecolour] (0,0) -- (1,0);
      \\draw[\\ganttdatelinecolour] (0,1+\\ganttntasks) -- (1,1+\\ganttntasks);
    \\end{pgfonlayer}
  %s
  %s
  %s
  \\end{tikzpicture}" projecttime ntasks tasks milestones dates))

Available languages

From Org's core

Language	Identifier	Language	Identifier
Asymptote	asymptote	Awk	awk
Emacs Calc	calc	C	C
C++	C++	Clojure	clojure
CSS	css	ditaa	ditaa
Graphviz	dot	Emacs Lisp	emacs-lisp
gnuplot	gnuplot	Haskell	haskell
Javascript	js	LaTeX	latex
Ledger	ledger	Lisp	lisp
Lilypond	lilypond	MATLAB	matlab
Mscgen	mscgen	Objective Caml	ocaml
Octave	octave	Org-mode	org
		Perl	perl
Plantuml	plantuml	Python	python
R	R	Ruby	ruby
Sass	sass	Scheme	scheme
GNU Screen	screen	shell	sh
SQL	sql	SQLite	sqlite

From Org's contrib/babel/langs

• ob-oz.el, by Torsten Anders and Eric Schulte
• ob-fomus.el, by Torsten Anders