Re: [Orgmode] [babel] exports, caching, remote execution

[David Maus]

Eric Schulte wrote:

Is scpc in the line above a transport protocol?  Maybe this should be
an org-mode wide features, i.e. the ability to resolve remote file
references with C-c C-o and on export.  Does that sound reasonable, and
would it take care of the need in this particular case?

I've created two IDEA issue in the issue file for this and another
operation on links especially during export: Link resolving and link
dereferencing.

Just out of my head without many thoughs about how to implement:

1.

Following the URI specs (RFC 3986) resolving and dereferencing means:

the process of determining an access mechanism and the appropriate
parameters necessary to dereference a URI (sc. resolving, D.M.); this
resolution may require several iterations.  To use that access
mechanism to perform an action on the URI's resource is to
dereference the URI. (1.2.2)

The basic idea is, that an Org mode link is a URI identifying a
resource; upon export it might be necessary or desired to provide
either an access mechanism suitable for the output format to access
the entity referenced by the URI or another URI (see below).

E.g.: An info reference to the Org mode manual [[info:org]] could be
resolved to a web link [[http://orgmode.org/manual/]] when exporting
to html.

Resolving is already done for files when exporting to html:
[[file:foo.baz]] is resolved to a relative web link, pointing to
foo.baz.

Dereferencing a link like

[[file:/scpc:u...@example.com:/users/home/user/test.png]]

could or would hence be part of resolving a file link.  It fetches the
resource (test.png), puts it into current directory and returns a link
suitable for the export context.

Another example would be a hypothetical Org mode link type rfc that
opens and stores links to RFCs using rfcview-mode.

When exporting an Org mode document to html, the function
`org-rfc-resolve-link' is called and returns a web link pointing to a
web resource of the RFC.  When exporting to latex, the function
`org-rfc-resolve-link' returns a link of type bib with the BibTeX
key of the RFC (e.g. rfc:4287 - bib:RFC4287), assuming that a
reference to a RFC in a LaTeX document is a bibliographic reference.

2.

To complete this way of link handling we require a third function:
Link markup.  An Org mode link handler may provide a markup-link
function that takes the exporting context and the link and returns
suitable markup of LINK in CONTEXT.

E.g. the handler for BibTeX links provides the function
`org-bib-markup-link' that returns proper markup of a bibliographic
reference.  In context of LaTeX export his would be a \cite command
with the BibTeX key of the bib link (bib:RFC4287 - \cite{4287}).

3.

For the sake of Lispness and to avoid repeated parsing, we define a
Lisp representation of an Org link to be:

((TYPE AI RESOURCE) . PROPS)

Where

  - TYPE :: Is a symbol of the type (scheme) of the link

  - RESOURCE :: Is the path or name of the referenced resource

  - AI :: Is t, if RESOURCE contains an authority, otherwise it is nil.

  Cf. RFC3986, 3.2; in the written representation of a URI the
  presence of an authority is indicated by the two slashes
  after the colon.

  - PROPS :: Is a property list of additional link properties
 (e.g. description)

Examples:

  - [[http://orgmode.org/manual/][Org mode manual]] is represented as:

((http t orgmode.org/manual/) . (:description Org mode manual))

  - [[info:org][Org mode manual]] is represented as

((info nil org) . (:description Org mode manual))

  - [[file:foo/baz.org]] is represented as

((file nil foo/baz.org))

Having this, resolving a link is modifying TYPE, RESOURCE and AI.

E.g. ((file nil foo/baz.org)) - ((http nil foo/baz.html))

 ((file nil /scp:u...@example.com:/users/home/user/test.png))

 - ((file nil test.png)) [dereferenced]

 - ((http nil test.png)) [finally resolved]

4.

The question of how to actually resolve a link is up to the respective
link handler and I am not sure how to provide easy customization of
such a system.

Comments are welcome,

 -- David


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[Orgmode] [babel] exports, caching, remote execution

[Austin Frank]

Hey all--

Two (hopefully quick) questions:

1) Does the exporter respect the :cache argument?  When I evaluate a
   buffer, I can tell that cached blocks are not re-run, as expected.
   When I export to \LaTeX or PDF, it seems that all blocks in the file
   are re-run.  Is there a way to force the exporter to respect caching?

2) Is there a way to generate graphical output on a remote host and
   still have it included in export?  A block like

   #+BEGIN_SRC R :exports results :dir /u...@example.com: :file test.png
   plot(my-object)
   #+END_SRC
   
   Gives me
   
   #+results:
   [[file:/scpc:u...@example.com:/users/home/user/test.png]]

   When I export to latex or pdf, the graphic isn't included because the
   file for export is local but the graphic is remote.  Is there a way
   to include remotely generated graphics in a locally exported file?
   Something like downloading via scp before exporting?


Thanks for any help,
/au
   
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Re: [Orgmode] [babel] exports, caching, remote execution

[Eric Schulte]

Hi Austin,

Austin Frank austin.fr...@gmail.com writes:

 Hey all--

 Two (hopefully quick) questions:

 1) Does the exporter respect the :cache argument?  When I evaluate a
buffer, I can tell that cached blocks are not re-run, as expected.
When I export to \LaTeX or PDF, it seems that all blocks in the file
are re-run.  Is there a way to force the exporter to respect caching?


I believe the exporter does respect caching, the following minimal
example worked (i.e. was not re-run) for me on export to html.  Could
you provide an example that demonstrates the problem?

--8---cut here---start-8---
** cache on export
do we export cached blocks

#+begin_src sh :cache yes :exports results
  date
#+end_src

#+results[06ed73c6d8d022cf9c323d92af885952865add17]:
: Thu Jun 17 07:35:19 PDT 2010
--8---cut here---end---8---


 2) Is there a way to generate graphical output on a remote host and
still have it included in export?

Not that I'm currently aware of.  Dan has handled most of the remote
execution work so he may know more than me in this regard.

A block like

#+source: rplot
#+BEGIN_SRC R :exports results :dir /u...@example.com: :file test.png
plot(my-object)
#+END_SRC

Gives me

#+results:
[[file:/scpc:u...@example.com:/users/home/user/test.png]]


Is scpc in the line above a transport protocol?  Maybe this should be
an org-mode wide features, i.e. the ability to resolve remote file
references with C-c C-o and on export.  Does that sound reasonable, and
would it take care of the need in this particular case?


When I export to latex or pdf, the graphic isn't included because
the file for export is local but the graphic is remote.  Is there a
way to include remotely generated graphics in a locally exported
file?  Something like downloading via scp before exporting?


A block like the following may be an acceptable workaround in the near
term (notice I named your block above).

#+begin_src sh :file test.png :var remote=rplot :exports results
  scp $remote ./test.png
#+end_src



 Thanks for any help,
 /au

Thanks -- Eric

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