#+OPTIONS:    H:3 num:nil toc:t
#+TITLE: org-babel --- facilitating communication between programming languages and people
#+SEQ_TODO:  TODO PROPOSED | DONE DEFERRED REJECTED
#+STARTUP: oddeven

* Introduction

Org-Babel enables *communication* between programming languages and
between people.

Org-Babel provides:
- communication between programs :: Data passes seamlessly between
     different programming languages, text, and tables.
- communication between people :: Data and calculations are embedded
     in the same document as notes explanations and reports.

** communication between programs

Org-Mode supports embedded blocks of source code (in any language)
inside of Org documents.  Org-Babel allows these blocks of code to be
executed from within Org-Mode with natural handling of their inputs
and outputs.

*** simple execution
with both scalar, file, and table output


*** reading information from tables


*** reading information from other source blocks (disk usage in your home directory)

This will work for Linux and Mac users, not so sure about shell
commands for windows users.

To run place the cursor on the =#+begin_src= line of the source block
labeled directory-pie and press =\C-c\C-c=.

#+srcname: directories
#+begin_src bash :results replace
cd ~ && du -sc * |grep -v total
#+end_src

#+resname: directories
|       64 | "Desktop"   |
| 11882808 | "Documents" |
|  8210024 | "Downloads" |
|   879800 | "Library"   |
|    57344 | "Movies"    |
|  7590248 | "Music"     |
|  5307664 | "Pictures"  |
|        0 | "Public"    |
|      152 | "Sites"     |
|        8 | "System"    |
|       56 | "bin"       |
|  3274848 | "mail"      |
|  5282032 | "src"       |
|     1264 | "tools"     |

#+srcname: directory-pie
#+begin_src R :var dirs = directories
pie(dirs[,1], labels = dirs[,2])
#+end_src


*** operations in/on tables

#+tblname: grades-table
| student | grade | letter |
|---------+-------+--------|
|       1 |    48 | F      |
|       2 |    30 | F      |
|       3 |     0 | F      |
|       4 |     1 | F      |
|       5 |    56 | F      |
|       6 |    46 | F      |
#+TBLFM: $2='(sbe random-score-generator)::$3='(sbe assign-grade (score $2))

#+srcname: assign-grade
#+begin_src ruby :var score=99
case score
   when 0..59: "F"
   when 60..69: "D"
   when 70..79: "C"
   when 80..89: "B"
   when 90..100: "A"
   else "Invalid Score"
end
#+end_src

#+srcname: random-score-generator
#+begin_src ruby 
rand(100)
#+end_src

#+srcname: show-distribution
#+begin_src R :var grades=grades-table
hist(grades[,2])
#+end_src


** communication between people
Quick overview of Org-Mode's exportation abilities, with links to the
online Org-Mode documentation, a focus on source-code blocks, and the
exportation options provided by Org-Babel.

*** Interactive tutorial
This would demonstrate applicability to Reproducible Research, and
Literate Programming.

*** Tests embedded in documentation
org-babels own functional tests are contained in a large org-mode
table, allowing the test suite to be run be evaluation of the table
and the results to be collected in the same table.


* Tasks [20/31]

** TODO resolve references to other buffers
   This would allow source blocks to call upon tables, source-blocks,
   and results in other buffers.
   
   See...
   - [[file:lisp/org-babel-ref.el::TODO%20allow%20searching%20for%20names%20in%20other%20buffers][org-babel-ref.el:searching-in-other-buffers]]
   - [[file:lisp/org-babel.el::defun%20org-babel%20find%20named%20result%20name][org-babel.el#org-babel-find-named-result]]

** TODO figure out how to handle graphic output
This is listed under [[* graphical output][graphical output]] in out objectives.

This should take advantage of the =:results file= option, and
languages which almost always produce graphical output should set
=:results file= to true by default.  That would handle placing these
results in the buffer.  Then if there is a combination of =silent= and
=file= =:results= headers we could drop the results to a temp buffer
and pop open that buffer...

** TODO share org-babel
how should we share org-babel?

- post to org-mode and ess mailing lists
- create a org-babel page on worg
- create a short screencast demonstrating org-babel in action

*** examples
we need to think up some good examples

**** interactive tutorials
This could be a place to use [[* org-babel assertions][org-babel assertions]].

for example the first step of a tutorial could assert that the version
of the software-package (or whatever) is equal to some value, then
source-code blocks could be used with confidence (and executed
directly from) the rest of the tutorial.

**** answering a text-book question w/code example
org-babel is an ideal environment enabling both the development and
demonstrationg of the code snippets required as answers to many
text-book questions.

**** something using tables
maybe something along the lines of calculations from collected grades

**** file sizes
Maybe something like the following which outputs sizes of directories
under the home directory, and then instead of the trivial =emacs-lisp=
block we could use an R block to create a nice pie chart of the
results.

#+srcname: sizes
#+begin_src bash :results replace
du -sc ~/*
#+end_src

#+begin_src emacs-lisp :var sizes=sizes :results replace
(mapcar #'car sizes)
#+end_src

** TODO command line execution
Allow source code blocks to be called form the command line.  This
will be easy using the =sbe= function in [[file:lisp/org-babel-table.el][org-babel-table.el]].

This will rely upon [[* resolve references to other buffers][resolve references to other buffers]].

** TODO inline source code blocks [3/5]
   Like the =\R{ code }= blocks

   not sure what the format should be, maybe just something simple
   like =src_lang[]{}= where lang is the name of the source code
   language to be evaluated, =[]= is optional and contains any header
   arguments and ={}= contains the code.

   (see [[* (sandbox) inline source blocks][the-sandbox]])

*** DONE evaluation with \C-c\C-c
Putting aside the header argument issue for now we can just run these
with the following default header arguments
- =:results= :: silent
- =:exports= :: results

*** DONE inline exportation
Need to add an interblock hook (or some such) through org-exp-blocks
*** DONE header arguments
We should make it possible to use header arguments.

*** TODO fontification
we should color these blocks differently

*** TODO refine html exportation
should use a span class, and should show original source in tool-tip

** TODO allow tables with hline to be passed as args into R
   This doesn't seem to work at the moment (example below). It would
   also be nice to have a natural way for the column names of the org
   table to become the column names of the R data frame, and to have
   the option to specify that the first column is to be used as row
   names in R (these must be unique). But this might require a bit of
   thinking about.


#+TBLNAME: egtable
| col1 | col2    | col3 |
|------+---------+------|
|    1 | 2       |    3 |
|    4 | schulte |    6 |

#+begin_src R var tabel=egtable
tabel
#+end_src

Another example is in the [[*operations%20in%20on%20tables][grades example]].

** TODO pass mutliple reference arguments into R
   Can we do this? I wasn't sure how to supply multiple 'var' header
   args. Just delete this TODO if I'm being dense.
** TODO Create objects in top level (global) environment in R?
   At the moment, objects created by computations performed in the
   code block are evaluated in the scope of the
   code-block-function-body and therefore disappear when the code
   block is evaluated {unless you employ some extra trickery like
   assign('name', object, env=globalenv()) }. I think it will be
   desirable to also allow for a style wherein objects that are
   created in one code block persist in the R global environment and
   can be re-used in a separate block.

   This is what Sweave does, and while I'm not saying we have to be
   the same as Sweave, it wouldn't be hard for us to provide the same
   behaviour in this case; if we don't, we risk undeservedly being
   written off as an oddity by some.

   IOW one aspect of org-babel is that of a sort of functional
   meta-programming language. This is crazy, in a very good
   way. Nevertheless, wrt R I think there's going to be a lot of value
   in providing for a working style in which the objects are stored in
   the R session, rather than elisp/org buffer. This will be a very
   familiar working style to lots of people.

   There are no doubt a number of different ways of accomplishing
   this, the simplest being a hack like adding

#+begin_src R
for(objname in ls())
    assign(objname, get(objname), envir=globalenv())
#+end_src

to the source code block function body. (Maybe wrap it in an on.exit() call).

However this may deserve to be thought about more carefully, perhaps
with a view to having a uniform approach across languages. E.g. shell
code blocks have the same semantics at the moment (no persistence of
variables across code blocks), because the body is evaluated in a new
bash shell process rather than a running shell. And I guess the same
is true for python. However, in both these cases, you could imagine
implementing the alternative in which the body is evaluated in a
persistent interactive session. It's just that it's particularly
natural for R, seeing as both ESS and org-babel evaluate commands in a
single persistent R session.

** PROPOSED support for passing paths to files between source blocks
Maybe this should be it's own result type (in addition to scalars and
vectors).  The reason being that some source-code blocks (for example
ditaa or anything that results in the creation of a file) may want to
pass a file path back to org-mode which could then be inserted into
the org-mode buffer as a link to the file...

This would allow for display of images upon export providing
functionality similar to =org-exp-blocks= only in a more general
manner.

** PROPOSED re-implement helper functions from org-R
Much of the power of org-R seems to be in it's helper functions for
the quick graphing of tables.  Should we try to re-implement these
functions on top of org-babel?

I'm thinking this may be useful both to add features to org-babel-R and
also to potentially suggest extensions of the framework.  For example
one that comes to mind is the ability to treat a source-code block
like a function which accepts arguments and returns results. Actually
this can be it's own TODO (see [[* source blocks as functions][source blocks as functions]]).

** DEFERRED use textConnection to pass tsv to R?
   When passing args from the org buffer to R, the following route is
   used: arg in buffer -> elisp -> tsv on file -> data frame in R. I
   think it would be possible to avoid having to write to file by
   constructing an R expression in org-babel-R-assign-elisp, something
   like this

#+begin_src emacs-lisp
(org-babel-R-input-command
 (format  "%s <- read.table(textConnection(\"%s\"), sep=\"\\t\", as.is=TRUE)"
	  name (orgtbl-to-tsv value '(:sep "\t" :fmt org-babel-R-quote-tsv-field))))
#+end_src

   I haven't tried to implement this yet as it's basically just
   fiddling with something that works. The only reason for it I can
   think of would be efficiency and I haven't tested that.

   This Didn't work after an initial test.  I still think this is a
   good idea (I also think we should try to do something similar when
   writing out results frmo R to elisp) however as it wouldn't result
   in any functional changes I'm bumping it down to deferred for
   now. [Eric]

for quick tests

#+tblname: quick-test
| 1 | 2 | 3 |

#+srcname: quick-test-src-blk
#+begin_src R :var vec=quick-test
mean(mean(vec))
#+end_src

: 2

** DEFERRED re-implement R evaluation using ess-command or ess-execute
   I don't have any complaints with the current R evaluation code or
   behaviour, but I think it would be good to use the ESS functions
   from a political point of view. Plus of course it has the normal
   benefits of an API (insulates us from any underlying changes etc). [DED]

   I'll look into this.  I believe that I looked at and rejected these
   functions initially but now I can't remember why.  I agree with
   your overall point about using API's where available.  I will take
   a look back at these and either switch to using the ess commands,
   or at least articulate under this TODO the reasons for using our
   custom R-interaction commands. [Eric]

   ess-execute

   Lets just replace =org-babel-R-input-command= with =ess-execute=.

   I tried this, and although it works in some situations, I find that
   =ess-command= will often just hang indefinitely without returning
   results.  Also =ess-execute= will occasionally hang, and pops up
   the buffer containing the results of the command's execution, which
   is undesirable.  For now these functions can not be used.  Maybe
   someone more familiar with the ESS code can recommend proper usage
   of =ess-command= or some other lower-level function which could be
   used in place of [[file:lisp/org-babel-R.el::defun%20org-babel%20R%20input%20command%20command][org-babel-R-input-command]].

*** ess functions
   
#+begin_quote ess-command
(ess-command COM &optional BUF SLEEP NO-PROMPT-CHECK)

Send the ESS process command COM and delete the output
from the ESS process buffer.  If an optional second argument BUF exists
save the output in that buffer. BUF is erased before use.
COM should have a terminating newline.
Guarantees that the value of .Last.value will be preserved.
When optional third arg SLEEP is non-nil, `(sleep-for (* a SLEEP))'
will be used in a few places where `a' is proportional to `ess-cmd-delay'.
#+end_quote

#+begin_quote ess-execute
(ess-execute COMMAND &optional INVERT BUFF MESSAGE)

Send a command to the ESS process.
A newline is automatically added to COMMAND.  Prefix arg (or second arg
INVERT) means invert the meaning of
`ess-execute-in-process-buffer'.  If INVERT is 'buffer, output is
forced to go to the process buffer.  If the output is going to a
buffer, name it *BUFF*.	 This buffer is erased before use.  Optional
fourth arg MESSAGE is text to print at the top of the buffer (defaults
to the command if BUFF is not given.)
#+end_quote

*** out current setup

    1) The body of the R source code block is wrapped in a function
    2) The function is called inside of a =write.table= function call
       writing the results to a table
    3) The table is read using =org-table-import=

** DEFERRED Rework Interaction with Running Processes [0/3]
*** TODO ability to select which of multiple sessions is being used
    Increasingly it is looking like we're going to want to run all
    source code blocks in comint buffer (sessions).  Which will have
    the benefits of
    1) allowing background execution
    2) maintaining state between source-blocks
       - allowing inline blocks w/o header arguments 

**** R sessions
     (like ess-switch-process in .R buffers)
     
     Maybe this could be packaged into a header argument, something
     like =:R_session= which could accept either the name of the
     session to use, or the string =prompt=, in which case we could use
     the =ess-switch-process= command to select a new process.
     
*** TODO evaluation of shell code as background process? 
    After C-c C-c on an R code block, the process may appear to
    block, but C-g can be used to reclaim control of the .org buffer,
    without interrupting the R evalution. However I believe this is not
    true of bash/sh evaluation. [Haven't tried other languages] Perhaps
    a solution is just to background the individual shell commands.

    The other languages (aside from emacs lisp) are run through the
    shell, so if we find a shell solution it should work for them as
    well.
    
    Adding an ampersand seems to be a supported way to run commands in
    the background (see [[http://www.emacswiki.org/emacs/ExecuteExternalCommand#toc4][external-commands]]).  Although a more extensible
    solution may involve the use of the [[elisp:(progn (describe-function 'call-process-region) nil)][call-process-region]] function.
    
    Going to try this out in a new file [[file:lisp/org-babel-proc.el][org-babel-proc.el]].  This should
    contain functions for asynchronously running generic shell commands
    in the background, and then returning their input.

**** partial update of org-mode buffer
    The sleekest solution to this may be using a comint buffer, and
    then defining a filter function which would incrementally interpret
    the results as they are returned, including insertion into the
    org-mode buffer.  This may actually cause more problems than it is
    worth, what with the complexities of identifying the types of
    incrementally returned results, and the need for maintenance of a
    process marker in the org buffer.

**** 'working' spinner
     It may be nice and not too difficult to place a spinner on/near the
     evaluating source code block

*** TODO conversion of output from interactive shell, R (and python) sessions to org-babel buffers
    [DED] This would be a nice feature I think. Although a org-babel purist
    would say that it's working the wrong way round... After some
    interactive work in a *R* buffer, you save the buffer, maybe edit
    out some lines, and then convert it to org-babel format for
    posterity. Same for a shell session either in a *shell* buffer, or
    pasted from another terminal emulator. And python of course.

** DONE ensure that table ranges work
when a table range is passed to org-babel as an argument, it should be
interpreted as a vector.

| 1 | 2 | simple       |
| 2 | 3 | Fixnum:1     |
| 3 | 4 | Array:123456 |
| 4 | 5 |              |
| 5 | 6 |              |
| 6 | 7 |              |
#+TBLFM: @1$3='(sbe simple-sbe-example (n 4))::@2$3='(sbe task-table-range (n @1$1..@6$1))::@3$3='(sbe task-table-range (n (@1$1..@6$1)))

#+srcname: simple-sbe-example
#+begin_src emacs-lisp 
"simple"
#+end_src

#+srcname: task-table-range
#+begin_src ruby :var n=simple-sbe-example
"#{n.class}:#{n}"
#+end_src

#+srcname: simple-results
#+begin_src emacs-lisp :var n=task-table-range(n=(1 2 3))
n
#+end_src

#+resname: simple-results
: Array:123

#+srcname: task-arr-referent
#+begin_src ruby :var ar=(1 2 3)
ar.size
#+end_src

#+resname: task-arr-referent
: 3

** DONE global variable indicating default to vector output
how about an alist... =org-babel-default-header-args= this may already
exist... just execute the following and all source blocks will default
to vector output

#+begin_src emacs-lisp 
(setq org-babel-default-header-args '((:results . "vector")))
#+end_src

** DONE name named results if source block is named
currently this isn't happening although it should be

#+srcname: test-naming-named-source-blocks
#+begin_src emacs-lisp 
:namer
#+end_src

#+resname: test-naming-named-source-blocks
: :namer
** DONE (simple caching) check for named results before source blocks
see the TODO comment in [[file:lisp/org-babel-ref.el::TODO%20This%20should%20explicitly%20look%20for%20resname%20lines%20before][org-babel-ref.el#org-babel-ref-resolve-reference]]
** DONE set =:results silent= when eval with prefix argument

#+begin_src emacs-lisp
'silentp
#+end_src
** DONE results-type header (vector/file) [3/3]
   In response to a point in Dan's email.  We should allow the user to
   force scalar or vector results.  This could be done with a header
   argument, and the default behavior could be controlled through a
   configuration variable.
   
#+srcname: task-trivial-vector
#+begin_src ruby :results replace vector
:scalar
#+end_src

#+resname:
| ":scalar" |

   since it doesn't make sense to turn a vector into a scalar, lets
   just add a two values...
   
   - vector :: forces the results to be a vector (potentially 1 dimensional)
   - file :: this throws an error if the result isn't a string, and
             tries to treat it as a path to a file.

   I'm just going to cram all of these into the =:results= header
   argument.  Then if we allow multiple header arguments it should
   work out, for example one possible header argument string could be
   =:results replace vector file=, which would *replace* any existing
   results forcing the results into an org-mode table, and
   interpreting any strings as file paths.

*** DONE multiple =:results= headers

#+srcname: multiple-result-headers
#+begin_src ruby :results replace silent
:schulte
#+end_src

#+resname:

*** DONE file result types
When inserting into an org-mode buffer create a link with the path
being the value, and optionally the display being the
=file-name-nondirectory= if it exists.

#+srcname: task-file-result
#+begin_src python :results replace file
"something"
#+end_src

#+resname:
[[something][something]]


This will be useful because blocks like =ditaa= and =dot= can return
the string path of their files, and can add =file= to their results
header.

*** DONE vector result types

#+srcname: task-force-results
#+begin_src emacs-lisp :results vector
8
#+end_src

#+resname:
| 8 |

** DONE results name
    In order to do this we will need to start naming our results.
    Since the source blocks are named with =#+srcname:= lines we can
    name results with =#+resname:= lines (if the source block has no
    name then no name is given to the =#+resname:= line on creation,
    otherwise the name of the source block is used).

    This will have the additional benefit of allowing results and
    source blocks to be located in different places in a buffer (and
    eventually in different buffers entirely).

#+srcname: developing-resnames
#+begin_src emacs-lisp  :results silent
'schulte
#+end_src

    Once source blocks are able to find their own =#+resname:= lines
    we then need to...

#+srcname: sbe-w-new-results
#+begin_src emacs-lisp :results replace
(sbe "developing-resnames")
#+end_src

#+resname:
: schulte

*** TODO change the results insertion functions to use these lines

*** TODO teach references to resolve =#+resname= lines.

** DONE org-babel tests org-babel [1/1]
since we are accumulating this nice collection of source-code blocks
in the sandbox section we should make use of them as unit tests.
What's more, we should be able to actually use org-babel to run these
tests.

We would just need to cycle over every source code block under the
sandbox, run it, and assert that the return value is equal to what we
expect.

I have the feeling that this should be possible using only org-babel
functions with minimal or no additional elisp.  It would be very cool
for org-babel to be able to test itself.

This is now done, see [[* Tests]].

*** DEFERRED org-babel assertions (may not be necessary)
These could be used to make assertions about the results of a
source-code block.  If the assertion fails then the point could be
moved to the block, and error messages and highlighting etc... could
ensue

** DONE make C-c C-c work anywhere within source code block?
   This seems like it would be nice to me, but perhaps it would be
   inefficient or ugly in implementation? I suppose you could search
   forward, and if you find #+end_src before you find #+begin_src,
   then you're inside one. [DED]

   Agreed, I think inside of the =#+srcname: line= would be useful as
   well.

#+srcname: testing-out-cc
#+begin_src emacs-lisp
'schulte
#+end_src

** DONE integration with org tables
We should make it easy to call org-babel source blocks from org-mode
table formulas.  This is practical now that it is possible to pass
arguments to org-babel source blocks.

See the related [[* (sandbox) integration w/org tables][sandbox]] header for tests/examples.

*** digging in org-table.el
In the past [[file:~/src/org/lisp/org-table.el::org%20table%20el%20The%20table%20editor%20for%20Org%20mode][org-table.el]] has proven difficult to work with.

Should be a hook in [[file:~/src/org/lisp/org-table.el::defun%20org%20table%20eval%20formula%20optional%20arg%20equation][org-table-eval-formula]].

Looks like I need to change this [[file:~/src/org/lisp/org-table.el::if%20lispp][if statement]] (line 2239) into a cond
expression.

** DONE source blocks as functions

Allow source code blocks to be called like functions, with arguments
specified.  We are already able to call a source-code block and assign
it's return result to a variable.  This would just add the ability to
specify the values of the arguments to the source code block assuming
any exist.  For an example see 

When a variable appears in a header argument, how do we differentiate
between it's value being a reference or a literal value?  I guess this
could work just like a programming language.  If it's escaped or in
quotes, then we count it as a literal, otherwise we try to look it up
and evaluate it.

** DONE folding of code blocks? [2/2]
   [DED] In similar way to using outline-minor-mode for folding function
   bodies, can we fold code blocks?  #+begin whatever statements are
   pretty ugly, and in any case when you're thinking about the overall
   game plan you don't necessarily want to see the code for each Step.

*** DONE folding of source code block
    Sounds good, and wasn't too hard to implement.  Code blocks should
    now be fold-able in the same manner as headlines (by pressing TAB
    on the first line).

*** REJECTED folding of results
    So, lets do a three-stage tab cycle... First fold the src block,
    then fold the results, then unfold.
    
    There's no way to tell if the results are a table or not w/o
    actually executing the block which would be too expensive of an
    operation.

** DONE selective export of text, code, figures
   [DED] The org-babel buffer contains everything (code, headings and
   notes/prose describing what you're up to, textual/numeric/graphical
   code output, etc). However on export to html / LaTeX one might want
   to include only a subset of that content. For example you might
   want to create a presentation of what you've done which omits the
   code.

   [EMS] So I think this should be implemented as a property which can
   be set globally or on the outline header level (I need to review
   the mechanics of org-mode properties).  And then as a source block
   header argument which will apply only to a specific source code
   block.  A header argument of =:export= with values of
   
   - =code= :: just show the code in the source code block
   - =none= :: don't show the code or the results of the evaluation
   - =results= :: just show the results of the code evaluation (don't
                  show the actual code)
   - =both= :: show both the source code, and the results

this will be done in [[* (sandbox) selective export][(sandbox) selective export]].

** DONE a header argument specifying silent evaluation (no output)
This would be useful across all types of source block.  Currently
there is a =:replace t= option to control output, this could be
generalized to an =:output= option which could take the following
options (maybe more)

- =t= :: this would be the default, and would simply insert the
         results after the source block
- =replace= :: to replace any results which may already be there
- =silent= :: this would inhibit any insertion of the results

This is now implemented see the example in the [[* silent evaluation][sandbox]]

** DONE assign variables from tables in R
This is now working (see [[* (sandbox table) R][(sandbox-table)-R]]).  Although it's not that
impressive until we are able to print table results from R.

** DONE insert 2-D R results as tables
everything is working but R and shell

*** DONE shells

*** DONE R

This has already been tackled by Dan in [[file:existing_tools/org-R.el::defconst%20org%20R%20write%20org%20table%20def][org-R:check-dimensions]].  The
functions there should be useful in combination with [[http://cran.r-project.org/doc/manuals/R-data.html#Export-to-text-files][R-export-to-csv]]
as a means of converting multidimensional R objects to emacs lisp.

It may be as simple as first checking if the data is multidimensional,
and then, if so using =write= to write the data out to a temporary
file from which emacs can read the data in using =org-table-import=.

Looking into this further, is seems that there is no such thing as a
scalar in R [[http://tolstoy.newcastle.edu.au/R/help/03a/3733.html][R-scalar-vs-vector]].  In that light I am not sure how to
deal with trivial vectors (scalars) in R.  I'm tempted to just treat
them as vectors, but then that would lead to a proliferation of
trivial 1-cell tables...

** DONE allow variable initialization from source blocks
Currently it is possible to initialize a variable from an org-mode
table with a block argument like =table=sandbox= (note that the
variable doesn't have to named =table=) as in the following example

#+TBLNAME: sandbox
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src emacs-lisp :var table=sandbox :results replace
(message (format "table = %S" table))
#+end_src

: "table = ((1 2 3) (4 \"schulte\" 6))"

It would be good to allow initialization of variables from the results
of other source blocks in the same manner.  This would probably
require the addition of =#+SRCNAME: example= lines for the naming of
source blocks, also the =table=sandbox= syntax may have to be expanded
to specify whether the target is a source code block or a table
(alternately we could just match the first one with the given name
whether it's a table or a source code block).

At least initially I'll try to implement this so that there is no need
to specify whether the reference is to a table or a source-code block.
That seems to be simpler both in terms of use and implementation.

This is now working for emacs-lisp, ruby and python (and mixtures of
the three) source blocks.  See the examples in the [[* (sandbox) referencing other source blocks][sandbox]].

This is currently working only with emacs lisp as in the following
example in the [[* emacs lisp source reference][emacs lisp source reference]].


** TODO Add languages [0/5]
I'm sure there are many more that aren't listed here.  Please add
them, and bubble any that you particularly care about up to the top.

Any new language should be implemented in a org-babel-lang.el file.
Follow the pattern set by [[file:lisp/org-babel-script.el][org-babel-script.el]], [[file:lisp/org-babel-shell.el][org-babel-shell.el]] and
[[file:lisp/org-babel-R.el][org-babel-R.el]].

*** TODO perl
This could probably be added to [[file:lisp/org-babel-script.el][org-babel-script.el]]

*** TODO java

*** TODO ditaa
(see [[* file result types][file result types]])

*** TODO dot
(see [[* file result types][file result types]])

*** TODO asymptote
(see [[* file result types][file result types]])


* Bugs [11/14]

** TODO non-orgtbl formatted lists
for example

#+srcname: this-doesn't-match-orgtbl
#+begin_src emacs-lisp :results replace
'((:results . "replace"))
#+end_src

#+resname: this-doesn't-match-orgtbl

** TODO collapsing consecutive newlines in string output

#+srcname: multi-line-string-output
#+begin_src ruby :results replace
"the first line ends here


     and this is the second one

even a third"
#+end_src

#+resname:
: the first line ends here
: 	     and this is the second one
: 	return even a third

** TODO cursor movement when evaluating source blocks
   E.g. the pie chart example. Despite the save-window-excursion in
   org-babel-execute:R. (I never learned how to do this properly: org-R
   jumps all over the place...)

** DONE R-code broke on "org-babel" rename

#+srcname: bug-R-babels
#+begin_src R 
8 * 2
#+end_src

** DONE error on trivial R results

So I know it's generally not a good idea to squash error without
handling them, but in this case the error almost always means that
there was no file contents to be read by =org-table-import=, so I
think it's ok.

#+srcname: bug-trivial-r1
#+begin_src R :results replace
pie(c(1, 2, 3), labels = c(1, 2, 3))
#+end_src

#+srcname: bug-trivial-r2
#+begin_src R :results replace
8
#+end_src

#+resname: bug-trivial-r2
: 8

#+srcname: bug-trivial-r3
#+begin_src R :results replace
c(1, 2, 3)
#+end_src

#+resname: bug-trivial-r3
| 1 |
| 2 |
| 3 |

** DONE ruby new variable creation (multi-line ruby blocks)
Actually it looks like we were dropping all but the last line.

#+srcname: multi-line-ruby-test
#+begin_src ruby :var table=bug-numerical-table :results replace
total = 0
table.each{|n| total += n}
total/table.size
#+end_src

#+resname:
: 2

** DONE R code execution seems to choke on certain inputs
Currently the R code seems to work on vertical (but not landscape)
tables

#+srcname: little-fake
#+begin_src emacs-lisp 
"schulte"
#+end_src

#+begin_src R :var num=little-fake
num
#+end_src

#+resname:
: schulte
: 11
: 11
: 11
: schulte
: 9
: 9
: 11

#+srcname: set-debug-on-error
#+begin_src emacs-lisp :results silent
(setq debug-on-error t)
#+end_src

#+srcname: bug-numerical-table
#+begin_src emacs-lisp :results silent
'(1 2 3)
#+end_src

#+srcname: bug-R-number-evaluation
#+begin_src R :var table=bug-numerical-table :results replace
mean(mean(table))
#+end_src

#+resname:
: 2

#+tblname: bug-vert-table
| 1 |
| 2 |
| 3 |

#+srcname: bug-R-vertical-table
#+begin_src R :var table=bug-vert-table :results silent
mean(table)
#+end_src

** DEFERRED org bug/request: prevent certain org behaviour within code blocks
   E.g. [[]] gets recognised as a link (when there's text inside the
   brackets). This is bad for R code at least, and more generally
   could be argued to be inappropriate. Is it difficult to get org to
   ignore text in code blocks? [DED]
   
   I believe Carsten addressed this recently on the mailing list with
   the comment that it was indeed a difficult issue.  I believe this
   may be one area where we could wait for an upstream (org-mode) fix.
** DONE with :results replace, non-table output doesn't replace table output
   And vice versa. E.g. Try this first with table and then with len(table) [DED]
#+begin_src python :var table=sandbox :results replace
table
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |
: 2

Yes, this is certainly a problem.  I fear that if we begin replacing
anything immediately following a source block (regardless of whether
it matches the type of our current results) we may accidentally delete
hand written portions of the user's org-mode buffer.

I think that the best solution here would be to actually start
labeling results with a line that looks something like...

#+results: name

This would have a couple of benefits...
1) we wouldn't have to worry about possibly deleting non-results
   (which is currently an issue)
2) we could reliably replace results even if there are different types
3) we could reference the results of a source-code block in variable
   definitions, which would be useful if for example we don't wish to
   re-run a source-block every time because it is long-running.

Thoughts?  If no-one objects, I believe I will implement the labeling
of results.

** DONE extra quotes for nested string
Well R appears to be reading the tables without issue...

these *should* be quoted
#+srcname: ls
#+begin_src sh :results replace
ls
#+end_src

| "COPYING"          |
| "README.markdown"  |
| "block"            |
| "examples.org"     |
| "existing_tools"   |
| "intro.org"        |
| "org-babel"          |
| "rorg.org"         |
| "test-export.html" |
| "test-export.org"  |

#+srcname: test-quotes
#+begin_src ruby :var tab=ls
tab[1][0]
#+end_src

: README.markdown

#+srcname: test-quotes
#+begin_src R :var tab=ls
as.matrix(tab[2,])
#+end_src

: README.markdown

** DONE simple ruby arrays not working

As an example eval the following.  Adding a line to test

#+srcname: simple-ruby-array
#+begin_src ruby
[3, 4, 5]
#+end_src

#+srcname: ruby-array-test
#+begin_src ruby :var ar = simple-ruby-array
ar.first
#+end_src

** DONE space trailing language name
fix regexp so it works when there's a space trailing the language name

#+srcname: test-trailing-space
#+begin_src ruby 
:schulte
#+end_src

** DONE Args out of range error
   
The following block resulted in the error below [DED]. It ran without
error directly in the shell.
#+begin_src sh
cd ~/work/genopca
for platf in ill aff ; do
    for pop in CEU YRI ASI ; do
	rm -f $platf/hapmap-genos-$pop-all $platf/hapmap-rs-all
	cat $platf/hapmap-genos-$pop-* > $platf/hapmap-genos-$pop-all
	cat $platf/hapmap-rs-* > $platf/hapmap-rs-all
    done
done
#+end_src
  
 executing source block with sh...
finished executing source block
string-equal: Args out of range: "", -1, 0

the error =string-equal: Args out of range: "", -1, 0= looks like what
used to be output when the block returned an empty results string.
This should be fixed in the current version, you should now see the
following message =no result returned by source block=.

** DONE ruby arrays not recognized as such

Something is wrong in [[file:lisp/org-babel-script.el]] related to the
recognition of ruby arrays as such.

#+begin_src ruby :results replace
[1, 2, 3, 4]
#+end_src

| 1 | 2 | 3 | 4 |

#+begin_src python :results replace
[1, 2, 3, 4]
#+end_src

| 1 | 2 | 3 | 4 |


* Tests

Evaluate all the cells in this table for a comprehensive test of the
org-babel functionality.

*Note*: if you have customized =org-babel-default-header-args= then some
of these tests may fail.

#+TBLNAME: org-babel-tests
| functionality           | block                      | arg |    expected |     results | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| basic evaluation        |                            |     |             |             | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| emacs lisp              | basic-elisp                |     |           5 |           5 | pass |
| shell                   | basic-shell                |     |           6 |           6 | pass |
| ruby                    | basic-ruby                 |     |   org-babel |   org-babel | pass |
| python                  | basic-python               |     | hello world | hello world | pass |
| R                       | basic-R                    |     |          13 |          13 | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| tables                  |                            |     |             |             | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| emacs lisp              | table-elisp                |     |           3 |           3 | pass |
| ruby                    | table-ruby                 |     |       1-2-3 |       1-2-3 | pass |
| python                  | table-python               |     |           5 |           5 | pass |
| R                       | table-R                    |     |         3.5 |         3.5 | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| source block references |                            |     |             |             | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| all languages           | chained-ref-last           |     |       Array |       Array | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| source block functions  |                            |     |             |             | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| emacs lisp              | defun-fibb                 |     |       fibbd |       fibbd | pass |
| run over                | Fibonacci                  |   0 |           1 |           1 | pass |
| a                       | Fibonacci                  |   1 |           1 |           1 | pass |
| variety                 | Fibonacci                  |   2 |           2 |           2 | pass |
| of                      | Fibonacci                  |   3 |           3 |           3 | pass |
| different               | Fibonacci                  |   4 |           5 |           5 | pass |
| arguments               | Fibonacci                  |   5 |           8 |           8 | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| bugs and tasks          |                            |     |             |             | pass |
|-------------------------+----------------------------+-----+-------------+-------------+------|
| simple ruby arrays      | ruby-array-test            |     |           3 |           3 | pass |
| R number evaluation     | bug-R-number-evaluation    |     |           2 |           2 | pass |
| multi-line ruby blocks  | multi-line-ruby-test       |     |           2 |           2 | pass |
| forcing vector results  | test-forced-vector-results |     |       Array |       Array | pass |
#+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))

** basic tests

#+srcname: basic-elisp
#+begin_src emacs-lisp :results silent
(+ 1 4)
#+end_src

#+srcname: basic-shell
#+begin_src sh :results silent
expr 1 + 5
#+end_src


#+srcname: basic-ruby
#+begin_src ruby :results silent
"org-babel"
#+end_src

#+srcname: basic-python
#+begin_src python :results silent
'hello world'
#+end_src

#+srcname: basic-R
#+begin_src R :results silent
b <- 9
b + 4
#+end_src

** read tables

#+tblname: test-table
| 1 | 2 | 3 |
| 4 | 5 | 6 |

#+srcname: table-elisp
#+begin_src emacs-lisp :results silent :var table=test-table
(length (car table))
#+end_src

#+srcname: table-ruby
#+begin_src ruby :results silent :var table=test-table
table.first.join("-")
#+end_src

#+srcname: table-python
#+begin_src python :var table=test-table
table[1][1]
#+end_src

#+srcname: table-R
#+begin_src R :var table=test-table
mean(mean(table))
#+end_src

** references

Lets pass a references through all of our languages...

Lets start by reversing the table from the previous examples

#+srcname: chained-ref-first
#+begin_src python :var table = test-table
table.reverse
#+end_src

Take the first part of the list

#+srcname: chained-ref-second
#+begin_src R :var table = chained-ref-first
table[1]
#+end_src

Turn the numbers into string

#+srcname: chained-ref-third
#+begin_src emacs-lisp :var table = chained-ref-second
(mapcar (lambda (el) (format "%S" el)) table)
#+end_src

and Check that it is still a list

#+srcname: chained-ref-last
#+begin_src ruby :var table=chained-ref-third
table.class.name
#+end_src

** source blocks as functions

#+srcname: defun-fibb
#+begin_src emacs-lisp :results silent
(defun fibbd (n) (if (< n 2) 1 (+ (fibbd (- n 1)) (fibbd (- n 2)))))
#+end_src

#+srcname: fibonacci
#+begin_src emacs-lisp :results silent :var n=7
(fibbd n)
#+end_src

** sbe tests
Testing the insertion of results into org-mode tables.

#+srcname: multi-line-output
#+begin_src ruby :results replace
"the first line ends here


     and this is the second one

even a third"
#+end_src

#+resname:
: the first line ends here
: 	     and this is the second one
: 	return even a third

#+srcname: multi-line-error
#+begin_src ruby :results replace
raise "oh nooooooooooo"
#+end_src

#+resname:
: -:5: warning: parenthesize argument(s) for future version
: -:5:in `main': oh nooooooooooo (RuntimeError)
: 	from -:8

| the first line ends here... | -:5: warning: parenthesize argument(s) for future version... |
#+TBLFM: $1='(sbe "multi-line-output")::$2='(sbe "multi-line-error")

** forcing results types tests

#+srcname: test-trivial-vector
#+begin_src emacs-lisp :results vector silent
8
#+end_src

#+srcname: test-forced-vector-results
#+begin_src ruby :var triv=test-trivial-vector :results silent
triv.class.name
#+end_src


* Sandbox
  :PROPERTIES:
  :CUSTOM_ID: sandbox
  :END:
To run these examples evaluate [[file:lisp/org-babel-init.el][org-babel-init.el]]

** org-babel.el beginning functionality

#+begin_src sh  :results replace
date
#+end_src

: Thu May 14 18:52:25 EDT 2009

#+begin_src ruby
Time.now
#+end_src

: Thu May 14 18:59:09 -0400 2009

#+begin_src python
"Hello World"
#+end_src

: Hello World


** org-babel-R

#+begin_src R :results replace
a <- 9
b <- 16
a + b
#+end_src

: 25

#+begin_src R
hist(rgamma(20,3,3))
#+end_src


** org-babel plays with tables
Alright, this should demonstrate both the ability of org-babel to read
tables into a lisp source code block, and to then convert the results
of the source code block into an org table.  It's using the classic
"lisp is elegant" demonstration transpose function.  To try this
out...

1. evaluate [[file:lisp/org-babel-init.el]] to load org-babel and friends
2. evaluate the transpose definition =\C-c\C-c= on the beginning of
   the source block
3. evaluate the next source code block, this should read in the table
   because of the =:var table=previous=, then transpose the table, and
   finally it should insert the transposed table into the buffer
   immediately following the block

*** Emacs lisp

#+begin_src emacs-lisp :results silent
(defun transpose (table)
  (apply #'mapcar* #'list table))
#+end_src


#+TBLNAME: sandbox
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src emacs-lisp :var table=sandbox :results replace
(transpose table)
#+end_src


#+begin_src emacs-lisp
'(1 2 3 4 5)
#+end_src

| 1 | 2 | 3 | 4 | 5 |

*** Ruby and Python

#+begin_src ruby :var table=sandbox :results replace
table.first.join(" - ")
#+end_src

: "1 - 2 - 3"

#+begin_src python :var table=sandbox :results replace
table[0]
#+end_src

| 1 | 2 | 3 |

#+begin_src ruby :var table=sandbox :results replace
table
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |

#+begin_src python :var table=sandbox :results replace
len(table)
#+end_src

: 2

| "__add__" | "__class__" | "__contains__" | "__delattr__" | "__delitem__" | "__delslice__" | "__doc__" | "__eq__" | "__format__" | "__ge__" | "__getattribute__" | "__getitem__" | "__getslice__" | "__gt__" | "__hash__" | "__iadd__" | "__imul__" | "__init__" | "__iter__" | "__le__" | "__len__" | "__lt__" | "__mul__" | "__ne__" | "__new__" | "__reduce__" | "__reduce_ex__" | "__repr__" | "__reversed__" | "__rmul__" | "__setattr__" | "__setitem__" | "__setslice__" | "__sizeof__" | "__str__" | "__subclasshook__" | "append" | "count" | "extend" | "index" | "insert" | "pop" | "remove" | "reverse" | "sort" |

*** (sandbox table) R

#+TBLNAME: sandbox_r
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src R :results replace
x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
x
#+end_src

| -3.35473133869346 |
|    -2.45714878661 |
| -3.32819924928633 |
| -2.97310212756194 |
| -2.09640758369576 |
| -5.06054014378736 |
| -2.20713700711221 |
| -1.37618039712037 |
| -1.95839385821742 |
| -3.90407396475502 |
|  2.51168071590226 |
|  3.96753011570494 |
|  3.31793212627865 |
|  1.99829753972341 |
|  4.00403686419829 |
|  4.63723764452927 |
|  3.94636744261313 |
|  3.58355906547775 |
|  3.01563442274226 |
|   1.7634976849927 |

#+begin_src R var tabel=sandbox_r :results replace
tabel
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |

*** shell
Now shell commands are converted to tables using =org-table-import=
and if these tables are non-trivial (i.e. have multiple elements) then
they are imported as org-mode tables...

#+begin_src sh :results replace
ls -l
#+end_src

| "total"      | 208 | ""    | ""    |    "" |   "" | "" | ""                |
| "-rw-r--r--" |   1 | "dan" | "dan" |    57 | 2009 | 15 | "block"           |
| "-rw-r--r--" |   1 | "dan" | "dan" | 35147 | 2009 | 15 | "COPYING"         |
| "-rw-r--r--" |   1 | "dan" | "dan" |   722 | 2009 | 18 | "examples.org"    |
| "drwxr-xr-x" |   4 | "dan" | "dan" |  4096 | 2009 | 19 | "existing_tools"  |
| "-rw-r--r--" |   1 | "dan" | "dan" |  2207 | 2009 | 14 | "intro.org"       |
| "drwxr-xr-x" |   2 | "dan" | "dan" |  4096 | 2009 | 18 | "org-babel"         |
| "-rw-r--r--" |   1 | "dan" | "dan" |   277 | 2009 | 20 | "README.markdown" |
| "-rw-r--r--" |   1 | "dan" | "dan" | 11837 | 2009 | 18 | "rorg.html"       |
| "-rw-r--r--" |   1 | "dan" | "dan" | 61829 | 2009 | 19 | "#rorg.org#"      |
| "-rw-r--r--" |   1 | "dan" | "dan" | 60190 | 2009 | 19 | "rorg.org"        |
| "-rw-r--r--" |   1 | "dan" | "dan" |   972 | 2009 | 11 | "test-export.org" |


** silent evaluation

#+begin_src ruby
:im_the_results
#+end_src

: :im_the_results

#+begin_src ruby :results silent
:im_the_results
#+end_src

#+begin_src ruby :results replace
:im_the_results_
#+end_src

: :im_the_results_


** (sandbox) referencing other source blocks
Doing this in emacs-lisp first because it's trivial to convert
emacs-lisp results to and from emacs-lisp.

*** emacs lisp source reference
This first example performs a calculation in the first source block
named =top=, the results of this calculation are then saved into the
variable =first= by the header argument =:var first=top=, and it is
used in the calculations of the second source block.

#+SRCNAME: top
#+begin_src emacs-lisp
(+ 4 2)
#+end_src

#+begin_src emacs-lisp :var first=top :results replace
(* first 3)
#+end_src

: 18

This example is the same as the previous only the variable being
passed through is a table rather than a number.

#+begin_src emacs-lisp :results silent
(defun transpose (table)
  (apply #'mapcar* #'list table))
#+end_src

#+TBLNAME: top_table
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+SRCNAME: second_src_example
#+begin_src emacs-lisp :var table=top_table
(transpose table)
#+end_src

#+begin_src emacs-lisp :var table=second_src_example :results replace
(transpose table)
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |
*** ruby python
Now working for ruby

#+srcname: start
#+begin_src ruby
89
#+end_src

#+begin_src ruby :var other=start :results replace
2 * other
#+end_src

and for python

#+SRCNAME: start_two
#+begin_src python
98
#+end_src

#+begin_src python :var another=start_two :results replace
another*3
#+end_src

*** mixed languages
Since all variables are converted into Emacs Lisp it is no problem to
reference variables specified in another language.

#+SRCNAME: ruby-block
#+begin_src ruby
2
#+end_src

#+SRCNAME: lisp_block
#+begin_src emacs-lisp :var ruby-variable=ruby-block
(* ruby-variable 8)
#+end_src

#+begin_src python :var lisp_var=lisp_block
lisp_var + 4
#+end_src

: 20

*** R

#+srcname: first_r
#+begin_src R :results replace
a <- 9
a
#+end_src

: 9

#+begin_src R :var other=first_r :results replace
other + 2
#+end_src

: 11


** (sandbox) selective export

For exportation tests and examples see (including exportation of
inline source code blocks) [[file:test-export.org]]


** (sandbox) source blocks as functions

#+srcname: default
#+begin_src emacs-lisp :results silent
5
#+end_src

#+srcname: triple
#+begin_src emacs-lisp :var n=default :results replace
(* 3 n)
#+end_src

: 15

#+begin_src emacs-lisp :var result=triple(n=3, m=98) :results replace
result
#+end_src

: 294

The following just demonstrates the ability to assign variables to
literal values, which was not implemented until recently.

#+begin_src ruby :var num="eric" :results replace
num+" schulte "
#+end_src

: "eric schulte "


** (sandbox) inline source blocks

This is an inline source code block src_ruby{1 + 6}.  And another
source block with text output src_emacs-lisp{"eric"}.

This is an inline source code block with header
arguments.  src_ruby[:var n=fibbd( n = 0 )]{n}


** (sandbox) integration w/org tables

#+begin_src emacs-lisp :results silent
(defun fibbd (n) (if (< n 2) 1 (+ (fibbd (- n 1)) (fibbd (- n 2)))))
#+end_src

#+srcname: fibbd
#+begin_src emacs-lisp :var n=4 :results silent
(fibbd n)
#+end_src

#+begin_src emacs-lisp :results silent
(mapcar #'fibbd '(0 1 2 3 4 5 6 7 8))
#+end_src

Something is not working here.  The function `sbe ' works fine when
called from outside of the table (see the source block below), but
produces an error when called from inside the table.  I think there
must be some narrowing going on during intra-table emacs-lisp
evaluation.

| original | fibbd |
|----------+-------|
|        0 |     1 |
|        1 |     1 |
|        2 |     2 |
|        3 |     3 |
|        4 |     5 |
|        5 |     8 |
|        6 |    13 |
|        7 |    21 |
|        8 |    34 |
|        9 |    55 |
#+TBLFM: $2='(sbe "fibbd" (n $1))

silent-result

#+begin_src emacs-lisp :results silent
(sbe 'fibbd (n "8"))
#+end_src


* Buffer Dictionary
 LocalWords:  DBlocks dblocks org-babel el eric fontification