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

#+title:    The Library of Babel
#+author:     Org-mode People
#+STARTUP:  odd hideblocks

* 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 [[file:~/src/worg/worg-git.org::contribute-to-worg][contribute them]] to
  worg.
  
  The raw Org-mode text of this file can be downloaded at
  [[repofile:contrib/babel/library-of-babel.org][library-of-babel.org]]

* Simple
A collection of simple utility functions

#+srcname: echo
#+begin_src emacs-lisp :var input="echo'd"
  input
#+end_src

* 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.
#+srcname: read
#+begin_src emacs-lisp :var file="" :var format=""
  (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)))
#+end_src

Write =data= to a file at =file=.  If =data= is a list, then write it
as a table in traditional Org-mode table syntax.
#+srcname: write
#+begin_src emacs-lisp :var data="" :var file="" :var ext='()
  (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
#+end_src

** remote files
**** json
Read local or remote file in [[http://www.json.org/][json]] format into emacs-lisp objects.
#+srcname: json
#+begin_src emacs-lisp :var file='() :var url='()
  (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))))
#+end_src

**** Google docs
The following code blocks make use of the [[http://code.google.com/p/googlecl/][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.
#+source: gdoc-read
#+begin_src emacs-lisp :var title="example" :var format="csv"
  (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)))
#+end_src

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.
#+source: gdoc-write
#+begin_src emacs-lisp :var title="babel-upload" :var data=fibs(n=10) :results silent
  (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)))
#+end_src

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.

#+srcname: R-plot(data=R-plot-example-data)
#+begin_src R
plot(data)
#+end_src

#+tblname: R-plot-example-data
| 1 |  2 |
| 2 |  4 |
| 3 |  9 |
| 4 | 16 |
| 5 | 25 |

#+lob: R-plot(data=R-plot-example-data)

#+resname: R-plot(data=R-plot-example-data)
: nil

** Gnuplot

* Org reference
** headline references
#+source: headline
#+begin_src emacs-lisp :var headline=top :var file='()
  (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)))
#+end_src

#+call: headline(headline="headline references")

* Tables
** LaTeX Table export
*** booktabs
This block can be used to wrap a table in the latex =booktabs=
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                  |
| env   | optional environment, default to "tabular" |
| width | optional width specification string        |

#+srcname: booktabs
#+begin_src emacs-lisp :var table='((:head) hline (:body)) :var align='() :var env="tabular" :var width='() :noweb yes :results latex
  (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))))))
#+end_src

*** 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                                  |

#+srcname: longtable
#+begin_src emacs-lisp :var table='((:table)) :var align='() :var width='() :var hline="\\hline" :var firsthead='() :var head='() :var foot='() :var lastfoot='() :noweb yes :results latex
  (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)))))
#+end_src

** Elegant lisp for transposing a matrix.

#+tblname: transpose-example
| 1 | 2 | 3 |
| 4 | 5 | 6 |

#+srcname: transpose
#+begin_src emacs-lisp :var table=transpose-example
  (apply #'mapcar* #'list table)
#+end_src

#+resname:
| 1 | 4 |
| 2 | 5 |
| 3 | 6 |

* Misc

** File-specific Version Control logging
   :PROPERTIES:
   :AUTHOR: Luke Crook
   :END:

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.

#+source: vc-log
#+headers: :var limit=-1
#+headers: :var buf=(buffer-name (current-buffer))
#+begin_src emacs-lisp
  ;; 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)))))
#+end_src

** Trivial python code blocks
#+srcname: python-identity(a=1)
#+begin_src python
a
#+end_src

#+srcname: python-add(a=1, b=2)
#+begin_src python
a + b
#+end_src

* GANTT Charts

The =elispgantt= source block was sent to the mailing list by Eric
Fraga.  It was modified slightly by Tom Dye.
 
#+source: elispgantt
#+begin_src emacs-lisp :var table=gantttest
  (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))
#+end_src