Dealing with inter-org links vs #+include

[Brett Viren]

Hi,

I want what may be two conflicting things:

- Produce a monolithic HTML export of an main org file that #+include:'s
  other org files.

- Have links in the other org files that are valid both when the
  monolith is exported to HTML and when visiting the individual org
  files in Emacs.

Below is a simple test.  The "main.org" includes "a.org" and "b.org".
The "b.org" has two types of links.  The link:

  [[A][A by headline only]]

is valid in the HTML export of "main.org" but it is not valid for Emacs
visiting b.org (C-c C-o gives "No match - create this as a new
heading?").  And then vice versa for the link:

  [[file:a.org::*A][A by file with headline]]

I can follow that link in Emacs but it renders to an  with
"a.html#MissingReference".  And export fails outright if I do not
include

  #+options: broken-links:t


Is there a way I can have my cake and eat it too?  That is, how can I
make a link between "sub" org files that can be followed by Emacs and
also that produces a valid HTML link when the main.org is exported?

Thanks!
-Brett.


$ ls *.org
a.org  b.org  main.org

$ for n in *.org
  echo "=== $n ==="
  cat $n
  end
=== a.org ===
* A

This is A.
=== b.org ===
* B

This is B.  Links:
- [[file:a.org::*A][A by file with headline]].
- [[A][A by headline only]].
  
=== main.org ===
#+title: Main
#+options: broken-links:t

* Main

This is main.

* Includes

#+include: a.org
#+include: b.org

* Links

- A :: [[file:a.org]]

- B :: [[file:b.org]]


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Re: [O] Org agenda

[Brett Viren]

"M. P."  writes:

> I create a TODO and save the file but I can’t see the todo when I
> select todo view in agenda? What am I doing wrong?

Maybe your file is not in the org-agenda-files list.  If so, a quick
check is to visit the file and do "C-c [" (org-agenda-file-to-front).
Then, recheck your agenda todo view.

-Brett.


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Re: [O] why prepend "file://" to abs paths in html output?

[Brett Viren]

Hi Nicolas,

Nicolas Goaziou  writes:

> So, basically, upon exporting the following document to HTML:
>
>   #+html_link_root: /tmp/
>   [[/tmp/unicorn.jpg]]
>
> the link becomes
>
>   

Is this saying "subtract the value of 'html_link_root' from the Org link
to make its URL"?

If so, I think this would not be general enough to help some cases.  For
example, with Nikola+orgmode and with Nikola's "pretty URLs" option the
relative location between either the Org source or its generated HTML
and an image that they both link will differ.

Some details:

Nikola source wants this layout:

  /path/to/my/nikola/posts/my-blog-post.org
  /path/to/my/nikola/images/unicorn.jpg

The Org source generates to HTML which will be found at this URL path:

  /mysiteroot/posts/my-blog-post/index.html

So, right now, either the Org link to the image must be written to be
invalid (for Org):

  [[../../images/unicorn.jpg]]

Or, some mechanism needs to turn the valid Org link:

  [[../images/unicorn.jpg]]

into either:

  

or:

  

I guess I could use html_link_root set to "/path/to/my/nikola" but then
my Org source loses portability.

I think better would be able to explicitly state the desired URL path
for the HTML  like:

  #+html_url_path: /mysiteroot/images/unicorn.jpg
  [[../images/unicorn.jpg]]


-Brett.

PS: imo, in this example, I think the real solution is to make Nikola
allow for keeping org+img source together and to output org+img+html all
together in one web directory.


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Re: [O] Overriding org-html-headline or other export functions?

[Brett Viren]

Brett Viren <b...@bnl.gov> writes:

> Or, maybe you suggest I do direct "surgery" on the TEXT argument that
> gets passed in to the filter and insert the "..." that way?  I guess it
> could work to find the end of the "" opening tag and then insert
> my "..." part.  I'll try this approach.

Okay, this works but relies on searching through the HTML to find the
end of "" tag.  This feels like it will be error prone but so far
it seems to work when processing my manual.

In case it might help others, here is my filter:

  https://github.com/WireCell/wire-cell-docs/blob/master/manuals/publish.el#L7

My Elisp is bad, so maybe this is not done well

And, for completeness there is now also the export-as-html,
export-to-html and publish-to-html functions copied from ox-html and
tweaked for this custom backend.


Thanks for the nudges and help!  

-Brett.

Re: [O] Overriding org-html-headline or other export functions?

[Brett Viren]

Marcin Borkowski  writes:

> It's been a while since I did that, but AFAIR deriving a new, slightly
> midified backend may be exactly what you want, since you seem to need to
> modify just one of the exporter functions.

Right, by my concern is I'm copy-pasting a large function just to change
basically one line.

I understand that instead of simply stepping on org-* function namespace
with my copy, I can rename my copy and make a derived exporter with my
modified function registered as a filter.  But that doesn't get away
from now having a chunk of code that is at risk of diverging away as
Org's original develops further.

-Brett.

Re: [O] Overriding org-html-headline or other export functions?

[Brett Viren]

"Charles C. Berry"  writes:

> You do have that wrong.  This is exactly what export filters and
> derived backends are for.  In fact, you can use both.  For an example,
> see
>
> http://orgmode.org/worg/exporters/filter-markup.html
>
> You will want to change `latex' to `html' in the
>
>   `(org-export-define-derived-backend ...)'
>
> call and delete all filters except for `:filter-headline'.  And revise
> `ox-mrkup-filter-headline' accordingly.

Thanks for checking me on this, but I still don't see it.

If I understand, a derived HTML backend with my own filter-headline
would let me add my own extra HTML *outside* the "...",
"...", etc, HTML that is generated by the base
org-html-headline filter.  But for the output I want I need to add my
extra HTML *inside* the contents of the "..." tags.  And I
don't see an export filter for this "..." part.

Or, maybe you suggest I do direct "surgery" on the TEXT argument that
gets passed in to the filter and insert the "..." that way?  I guess it
could work to find the end of the "" opening tag and then insert
my "..." part.  I'll try this approach.

-Brett.

[O] Overriding org-html-headline or other export functions?

[Brett Viren]

Hi,

I am writing a manual in Org which gets exported/published to HTML and
styled with org-html-themes.  I want the HTML to include a little icon
next to each headline which is a direct link to the headline itself.
Basically, I want to rip off what GitHub does when it renders Org.

First, is there some way to achieve this headline link without
explicitly adding it in the Org text or diving into Org Elisp?

I couldn't find one so I took the latter route by copying out the whole
of org-html-headline into the Emacs init Elisp file I used for
publishing and fiddle with it until I got more or less what I wanted.
Here are the lines tweaked:

  https://github.com/WireCell/wire-cell-docs/blob/master/manuals/publish.el#L69

Here is an example of the result:

  http://www.phy.bnl.gov/~bviren/wirecell.github.io/manual.html

Is this copy+hack the proper way to tweak the exporting in this case?
In particular, I worry about my copy of org-html-headline diverging from
the real.


I read about export filters and extending an existing back-end, but I
think these do not apply, but maybe I have that wrong.

Thanks for any suggestions!

-Brett.

Re: [O] git and orgmode: teaching git a bit of orgmode syntax

[Brett Viren]

Karl Voit  writes:

> -* NEXT test with DAVdroid
> +* Lesestoff [1/26]:2read:
>  :PROPERTIES:
> -:CREATED:  [2016-05-08 Sun 12:51]
> +:CREATED: [2012-04-17 Tue 10:39]
> +:ARCHIVE:  %s_archive::* Lesestoff
> +:CATEGORY: reading
>  :END:

Without seeing before/after versions it's not clear that this diff is
somehow wrong.

Depending on the editing one does to a given file, a diff may seem "non
local" with some chunks appearing to undo something and others redoing
it.  This happens when parts of the file get rearranged.  For example,
do either of your headlines appear elsewhere in your diff with their
"+/-" signs reversed?

-Brett.


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Re: [O] XML dump of org file?

[Brett Viren]

Aaron Ecay  writes:

> Have a look at the org-element library,

Just to add, there are circular dependencies in this data structure due
to ":parent" and potentially some of the ":structure" elements.  They
obviously need to be broken to avoid infinite loops.

Here my hackish attempt to deal with this in order to dump org-element
to JSON:

  https://github.com/brettviren/joyful-web/blob/master/joy/org2json.el

See org-json-straigten-tree for how I nullified these elements.

-Brett.


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Re: [O] Open Peer-Review Reproducible Publication with Org and GRASS

[Brett Viren]

Thanks for your example.

A few ideas:

- When you begin developing your paper, or sometime before submission,
  make a break from your personal ~/.emacs.d/ environment and begin
  processing the .org in an explicitly configured Emacs session.  Submit
  the needed, minimal, paper-specific Emacs setup as part of the
  supplementary material.

- Bundle the document building into a shell script which calls Emacs so
  that you can assure that personal ~/.emacs.d/ is excluded and only the
  paper-specific Emacs setup is used.  It also helps users to rebuild
  the paper, especially if they may not yet be Emacs aficionados.

- Instead of multi-GB VM image, provide a few kB Dockerfile which can be
  used to build a Linux container with base OS and all required
  applications needed to run the Babel code blocks.

- The Dockerfile could go so far as to create a user account, get the
  supplementary material from a repository or the publisher's web page,
  unpack and run the shell script which calls Emacs to build the
  document.  If you go this far then in principle just this Dockerfile
  is enough to reproduce the paper - but this will rely on some binaries
  to remain available (Docker base OS images and OS packages).

The reliance on long-term availability of the Docker base OS image and
binary packages is problematic for long term automated reproducibility.
However, even after those bits disappear from the 'net the Dockerfile
serves as a concise and explicit recipe for future humans to follow.

-Brett.


Ken Mankoff  writes:

> Hi Org and GRASS lists,
>
> I just wanted to let these two lists know that I've just posted a
> paper written in Org and using GRASS (text-mode) and Python for the
> analysis. My goal was to create not just an open access publication,
> but a fully reproducible publication. This is an early announcement,
> and the paper may not pass peer review.
>
> The Supplemental Material is the Org file with all the code to
> generate the document, beginning with downloading the 3rd party data
> that is input to our analysis, the GRASS code to perform the analysis,
> and the Python code to regenerate the figures.
>
> I don't think I did a great job on the reproducible part because I
> have a highly customized .emacs, etc. All the information necessary to
> replicate the work should be in the Supplemental Material, but it
> might not be easy to do so. Anyway, I think it is a step in the right
> direction.
>
> To make it easier to reproduce... including my emacs.org seems
> overkill. Including a Virtual Machine that contains everything,
> including my ~/.emacs.d/ and all the software and data seems like the
> right thing to do, but journals don't want to host a 20 GB VM with the
> publication.
>
> Thanks to people on these two lists who have developed the software and 
> helped me use it.
>
>-k.
>
> http://www.the-cryosphere-discuss.net/tc-2016-113/


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Re: [O] Clocking work time vs. office time

[Brett Viren]

Marcin Borkowski  writes:

> On 2016-04-29, at 11:21, Michael Welle  wrote:
>
>> Marcin Borkowski  writes:
>> I assume that you use a laptop or some other portable device? In that
>> case you can grep the IP address (which might change when you change
>> workplaces) and timestamps from the log files (or create a script that
>> logs the IP address changes to an ORG file) and then somehow (coughcough)
>> integrate that into your report. 
>
> That's actually an interesting (and not standard) idea.  Even moreso
> because I'm writing a RescueTime-like time-tracking tool for Emacs,
> working (unlike Org's clocking) without manual intervention - recording
> the state of computer (i.e., current idle time, active X window, active
> Emacs buffer name and mode) at regular (or not) intervals and making
> reports.  I did not include any network-related info, but this would be
> easy to add.  Thanks, I'll definitely think about it!

Along similar lines, how about running a process on a computer near
where you dwell at work which watches for your mobile phone's bluetooth
ID.  Recording when your phone enters/exits its range will sample the
time you are physically present.  If you roam around at work you will
need to remember to visit the BT range at the start and at the end of
your day in order to get a full measure.  And, you'll need to process
the samples to pull out the earliest/latest times to calculate the time
present.  This post-processing can emit Org text or whatever format you
want.

Looking at what bluetooth stuff is available on Ubuntu, "bluemon" seems
perfect for the heavy lifting.  Your OS may vary.


There are also Android apps that do this kind of locating directly using
GPS/WiFi location and uploading the results to google drive or similar.
However, I've never managed to find one which I can make work reliably.

-Brett.


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Re: [O] Best way to create blog for company web site with Orgmode

[Brett Viren]

Rainer Hansen  writes:

> Sometimes I should read more carefully what I write. I want to use a
> static web site generator! So Wordpress is no option for me.

Ah, okay! That makes more sense.  One day I will also learn to read what
I write.  :)

> Of course I could use Bootstrap with an Org-based static site
> generator. However, I my thinking is that I need to do a lot of
> customizations to use it as a blogging engine. Perhaps I am wrong. I
> would be happy if someone on the mailing-list has done it and can show
> that it is quite straight forward to do.

Yes, this desire to have the HTML match the CSS (without touching the
CSS) is one thing that drove me to rolling my own generator.  I didn't
want to muck with Org HTML export to make that match happen.

In the end, I found that most of what I wanted from Bootstrap relates to
what I think of as "outer" HTML - the banner, nav bar, menus, table of
contents, etc.  It ends up mattering less to me for the "inner" HTML of
the actual blog post or page payload content.  

If ever I do need to, I'm prepared develop some code to do some
rewriting of Org HTML during the generation.

> Yes, easy is relative. What I mean is that I can set it up in less than
> 4 hours through configuration. I want to be able to reuse the visual
> theme implemented in CSS for the rest of the web site in the time limit
> mentioned before.

When my system has some more polish then maybe your 4 hour limit can be
satisfied.  Right now, being my only customer, it may not pass your
definition of "easy".  But, you are welcome to take a look and try.

> Could you please provide some links? I am especially interested in
> tutorials on setting them up.

I don't guarantee that it will live up to its name but here is my
generator:

  https://github.com/brettviren/joyful-web

It's mostly Python based and uses Jinja2 templates.  Emacs is used to
generate a JSON dump of the org-element tree, to produce the HTML body
text and to make a PDF.

I don't have many examples in the source but I do inside my actual Org
content area.  Some things to look at include the main config file:

  https://github.com/brettviren/org-pub/blob/master/joy.cfg

an example template:

  https://github.com/brettviren/org-pub/tree/master/templates/topic.html

and, maybe look at how I call "joy" to rebuild the site.  I use "waf" to
do that and its control file is:

  https://github.com/brettviren/org-pub/blob/master/wscript

I only have this working on my laptop now so I can't show you the
results at the moment.  

-Brett.


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Re: [O] Best way to create blog for company web site with Orgmode

[Brett Viren]

Rainer Hansen  writes:

> I wonder what is the best way to create a blog for a company website
> with Orgmode. I do not want to use a static web site generator. The
> design of the web site is relying on Bootstrap and customs CSS.

Just curious, why does wanting to use Bootstrap rule out an Org-based
static site generator for you?

I'm slowly developing just such a beast.  It Works For Me(TM) but is
still a bit raw for others unless they can deal with some Python
hacking and spotty documentation.

> It should be easy to setup and to maintain for me?

I think maybe you can better define what you mean by "easy"?  

In the end, developing my own generator was easier than trying to adapt
existing ones.  There are a lot of great ones out there, especially if
you expand to allow Markdown ones (either native authoring or using
Org's Markdown export), but none do exactly what I wanted.

-Brett.


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Re: [O] Code block returning code results formatted as another type of code block?

[Brett Viren]

"Charles C. Berry"  writes:

> Try `:wrap src json':

Works perfectly, thanks.  I had missed this in the manual, but it was
there for me all along!

  http://orgmode.org/manual/wrap.html

-Brett.


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[O] Code block returning code results formatted as another type of code block?

[Brett Viren]

Hi,

I have some shell command line program that spits out JSON.  I want Org
execute that command from a source block (of type "sh") and have the
result displayed as another source block of type "json".  I can almost
get all that working except the resulting block is also of type "sh":

I have:


#+BEGIN_SRC sh  :exports both :format json :results value code 
echo '{"foo":"bar", "baz":"quax"}'
#+END_SRC

#+RESULTS:
#+BEGIN_SRC sh
{"foo":"bar", "baz":"quax"}
#+END_SRC


But, instead, I want the result:


#+RESULTS:
#+BEGIN_SRC json
{"foo":"bar", "baz":"quax"}
#+END_SRC


Is there some arg to the initial source block which I'm missing?

I guessed with that ":format json" arg.  With or without it makes no
difference.


Thanks!
-Brett.


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Re: [O] Exporting a subtree

[Brett Viren]

Peter Davis  writes:

> For the first time, I'm trying to export just a single subtree of my overall 
> document, by typing
>
> C-c C-e C-s H O
>
> However, I get this error:
>
> apply: Wrong type argument: listp, #("Details, November 2015" 0 22 (:parent 
> (#0)))

FWIW, I had this problem on my home machine about a week ago or so.  I
messed around with different versions of org and org-plus-contrib
installed from package-list-packages and eventually got it to go away.
Sorry I don't recall the specifics.  But I just wanted to say it's not
just you.

Right now, on my work system your test succeeds:

Org-mode version 8.2.10 (8.2.10-41-g42228a-elpa @ 
/home/bviren/.emacs.d/elpa/org-20150622/)

-Brett.


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Re: [O] Bug: message after org-clock-in [8.2.10 (8.2.10-34-gc41bbc-elpa @ /home/torys/.emacs.d/elpa/org-20150223/)]

[Brett Viren]

torys.ander...@gmail.com (Tory S. Anderson) writes:

 I'd love to. Unfortunately, search engines were unable to give me
 decisive answer on what an ECM is.

Heh.  I guessed what it meant, but not what it stood for, and found:

  http://orgmode.org/worg/org-faq.html

Some users call this an ECM, a French acronym that means a
minimal complete example.

Cheers,
-Brett.

Re: [O] Executing org shell blocks on remote machine over ssh

[Brett Viren]

David Bjergaard davi...@duke.edu writes:

 I use org mode as a lab notebook.  I write org-src blocks to keep track
 of tasks I do at the command line, and then I copy paste them into the
 terminal.  I would really like to hit C-c C-c on the source block and
 have it executed on the remote machine.  I know that you can specify
 the remote machine according to [1], however the software I use requires
 a fairly complicated setup to get going.  

Is it just complicated, or is it also prohibitively long-running?

If just the former, you could maybe bundle the setup into some shell
script and source it in each of your sh source blocks.  Eg:

#+BEGIN_SRC sh :results output :dir /ssh:lycastus:/home/bviren
  /bin/pwd
  echo $HOSTNAME
  ls -l foo.sh
  echo ---
  cat foo.sh
  echo ---
  source ./foo.sh
  echo $FOO
#+END_SRC

#+RESULTS:
: /home/bviren
: lycastus
: -rw-rw-r-- 1 bviren bviren 16 Nov 18 10:27 foo.sh
: ---
: export FOO=bar
: 
: ---
: bar



If the setup is purely environmental, and it takes a long time to
perform, maybe you could do the set up once and then cache the resulting
environment using the output of env.


-Brett.


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Re: [O] Executing org shell blocks on remote machine over ssh

[Brett Viren]

David Bjergaard davi...@duke.edu writes:

 I know this is working against the grain of the literate programming
 paradigm where the document and the source code are coupled, and
 tangling the document produces a program that can be executed.  I'm just
 wondering if its possible.  If not that's fine.  Really I'm just trying
 to save myself a copy-paste (and the associated issues with it getting
 recorded in my .bash_history).

I usually come at it from the reproducible research angle which maybe
is more relaxed than literate programming.  In any case, I find it hard
to capture all the info needed to reproduce something and so I settle
for capturing as much as easily achievable - that is when I try at all
as capturing it in an RR org doc greatly increases the time I need to do
something.

Many of the software stacks I use also take significant time to
configure the end-user environment.  10 seconds is not unheard of and it
can be minutes if the stack lives on slow network disk.

I think the approach I suggested of caching the environment should work
for you.  Unfortunately, I do not know of a trivial, general way to do
this.  The env program comes close but does not spit out a format that
is immediately consumable by the shell.  In particular, spaces in
variable values confound it.  It also lacks the export keyword.  And,
in any case is only close to sh syntax.  Any exported functions also
have to be handled properly

In your shoes, I'd probably write a small Python script that dumps the
os.environ dictionary holding the environment of the caller into a
form suitable for consumption by your shell.  You can call this dumper
in a shell code block at the top of your org file and source the result
as the first line in each subsequent shell code block.

A starting point would be something like the following, but this does
not properly handle and sh functions defined.

#!/usr/bin/env python
import os
for k,v in os.environ.items():
print 'export %s=%s' % (k,v)



Good luck!
-Brett.




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Re: [O] org-mode for knowledge management

[Brett Viren]

Hi Louis,

Louis lbml...@hethcote.com writes:

 I've been using org-mode for a variety of purposes for a few years. I
 find that it suffers from the same problem that other such tools
 do. The problem is me. I can't remember week to week how I may have
 classified some scrap of information. Did I drop it into
 notes/someproduct.org or was it procedures/someprocess.org?

I hear you.  My strategy so far has been: just write org content and an
ideal lookup solution will eventually be found (via threads like this
one!).

This weekend I took a first step and *finally* got agenda-based
searching to work.  For better or worse, my setup intentionally spreads
org content over a few areas:

For a few explicit, global files (eg, todo.org)
  ~/org/*.org  

For daily, private notes:
  ~/org/web/notes//MM/DD/notes.org   

For a wiki-like blog / knowledge bank:
  ~/org-pub/topics/TOPIC/index.org

By default, my attempts with org agenda search was not finding files in
these areas.  Particularly the latter two were difficult for me to
figure out how to tell org about.  The final solution was to walk these
directories at initialization time and add all .org files found to
org-agenda-text-search-extra-files.  Here is the most concise way to do
that which I found after various searches:

(require 'find-lisp)
(setq  
 org-agenda-files (list ~/org)
 org-agenda-text-search-extra-files 
 (append
  (find-lisp-find-files ~/org-pub/topics/ \\.org$)
  (find-lisp-find-files ~/org/web/notes/ \\.org$))
)

If anyone knows better ways to do this, I'm all ears.  I'm particularly
wondering how long-running org sessions will handle newly created topics
or notes in this setup.

-Brett.


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Re: [O] Fwd: Cooperating with oneself using the cloud?

[Brett Viren]

Monroe, Will wtmonroe...@gmail.com writes:

 Thanks so much for your reply, Tim.  git-annex does seem like a
 possibility for syncing org-mode files but it appears that there's a
 lot to consider when setting it up.

This thread prompted me last weekend to try git-annex via its
assistant.  It was pretty painless to set up hosts where I could run a
local web browser.  I was also able to easily set up a remote annex on a
headless git/SSH server via the web app.

I followed this:

  http://git-annex.branchable.com/assistant/quickstart/

-Brett.


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Re: [O] Emacs server and org-protocol

[Brett Viren]

Alexis flexibe...@gmail.com writes:

 If i may ask, which email front-end were you using? (Gnus, perhaps?) i
 used to use notmuch.el, and currently use mu4e, and basically don't have
 this issue 

My GNUS + IMAP subprocess + Maildir used to lead to long wait times when
updating for new mail (g in Groups).  Things have now vastly improved
since moving my Maildirs to a SSD.

-Brett.


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Re: [O] Unit conversions and symbolic mathematics with Babel

[Brett Viren]

Hi,

die...@duenenhof-wilhelm.de (H. Dieter Wilhelm) writes:

   But what is missing is to assign variables within a source block
   
 #+BEGIN_SRC calc :var L1 = 5 mm 
 L2 := cvun( L1, m)
 #+END_SRC
   
   Unfortunately this is not working.  Do you have an idea how to
   implement this?

 - Are you using (better) alternatives?

I like Python and in Python I like Pint for units.

  http://pint.readthedocs.org

Below is an example org document that should run and shows a couple
ways to use snippets of Pint code to do unit conversion.  Not shown but
Pint Quantity objects support arithmetic so are useful for carrying
units through some calculation.

For assigning to variables - presumably for use in later blocks - maybe
you can investigate using the :session header argument to source blocks.


Have fun,
-Brett.

One way to install Pint is:

#+BEGIN_SRC sh :results silent
  pip install --user pint
#+END_SRC

Here is an example:

#+name: uconv
#+header: :var val=10m :var unit=inch 
#+BEGIN_SRC python
  import pint
  units = pint.UnitRegistry()
  return units.Quantity(val).to(unit)
#+END_SRC

#+RESULTS: uconv
: 393.700787402 inch

Now call =uconv= do to some other conversion:

#+call: uconv(2.54cm,inch)

#+RESULTS:
: 1.0 inch


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Re: [O] Possible to use src block to generate org headlines for export?

[Brett Viren]

Matt Lundin m...@imapmail.org writes:

 That sounds interesting. I look forward to hearing more!

It's not yet usable for anything real but I'm keeping the work here:

  https://github.com/brettviren/orgonpy

-Brett.


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Re: [O] Possible to use src block to generate org headlines for export?

[Brett Viren]

Matt Lundin m...@imapmail.org writes:

 Let's hope the real blog (when I get around to publishing it) is more
 interesting than the example above. ;)

Maybe it would be more convenient to add the meta-ness you want as
part of a new exporter process?  

-Brett.


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Re: [O] Possible to use src block to generate org headlines for export?

[Brett Viren]

Matt Lundin m...@imapmail.org writes:

 Brett Viren b...@bnl.gov writes:

 Maybe it would be more convenient to add the meta-ness you want as
 part of a new exporter process?  

 To change the meta wrappers for code block results, we would have to
 modify org babel (ob-core.el). 

Just to be clear (hopefully) I actually meant something different.  I
was suggesting to *not* use org babel to produce your extra headlines.
Rather, have whatever logic produces them reside in some new exporter.

I'm may be making incorrect guesses as to what you are actually going
for with these extra headlines.  You mentioning this is for a blog made
me think they are some kind of standard augmentation for every blog
post or something.  If not then I'm probably barking up the wrong tree.
But if so, putting them into an exporter seems apt.

This is an approach I'm taking in a JSON+HTML exporter (analogous to the
latex+pdf one) that I'm working on.  For example, I'd like to have a
tag cloud generated from tags on org headlines.  This tag cloud won't
explicitly exist on the org side.  Rather it will be implicitly produced
and updated by some (Python) code that runs as part of the JSON-HTML
stage of the exporter.

Cheers,
-Brett.


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Re: [O] org-redisplay-inline-images and export to HTML

[Brett Viren]

Nick Dokos ndo...@gmail.com writes:

 I think you'd be better off with the tip that Rick Frankel posted in
 the same thread:

 #+BEGIN_SRC emacs-lisp
 (add-hook 'org-babel-after-execute-hook
 (lambda () (org-display-inline-images nil t)))
 #+END_SRC

Thanks Nick (and Rick).  I changed this to use the re version:

#+BEGIN_SRC emacs-lisp
(add-hook 'org-babel-after-execute-hook
  (lambda () (org-redisplay-inline-images)))
#+END_SRC

and it works great!  

-Brett.


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[O] org-redisplay-inline-images and export to HTML

[Brett Viren]

Someone recently posted a tip to add

  :post (org-redisplay-inline-images)

to a SRC block which generates an image in order to freshen the Emacs
buffer with the regenerated image each time the block is executed.  It
works *almost* fine but I have two problems which I hope someone can
help with.


1) Priming-the-pump

I'm using a document containing a GraphViz graph and running dot on it:

--
#+BEGIN_SRC dot :cmd dot :cmdline -Tpng :file foo.png :exports results :post 
(org-redisplay-inline-images) 
  digraph foo {
rankdir=LR;
params - builders;
builders - objects;
objects - file;
  }
#+END_SRC
--

I do C-c C-c in the block and the buffer does not display any result.
I see the messages:

--
No images to display inline
executing Dot code block...
Wrote /tmp/babel-11819Iqr/ob-input-11819Lrv
org-babel-ref-resolve: Reference 'No images to display inline' not found in 
this buffer
--

If I do C-c hh to export to HTML I see:

--
org-babel-exp processing...
No images to display inline [2 times]
executing Dot code block...
Wrote /tmp/babel-11819Iqr/ob-input-11819kTR
org-babel-ref-resolve: Reference 'No images to display inline' not found in 
this buffer
--

And I get no HTML file produced.

If I now take out the :post and do C-c C-c I get this appearing just
after the SRC block as expected:

--
#+RESULTS:
[[file:foo.png]]
--

If I now add back the :post and do C-c C-c again I get the inlined
image.  I can now edit the SRC block and repeat the C-c C-c and I am
pleased to see the figure refresh each time.  It's great!  But, it needs
this pump priming.


2) Post-priming, still no HTML export

After this priming the pump is done the second problem is that still a
C-c hh does not produce an exported HTML file.  Similar messages:

--
org-babel-exp processing...
No images to display inline
Inline image display turned off
No images to display inline
executing Dot code block...
Wrote /tmp/babel-11819Iqr/ob-input-11819zYx
org-babel-ref-resolve: Reference 'No images to display inline' not found in 
this buffer
--

Finally, if I remove the :post but leave the #+RESULTS: I can do 
a successful C-c hh.  

So, the upshot is I have to keep adding and removing the :post to make
things work in different contexts.  This is obviously not so smooth.


Is there some way to both have my cake an eat it too?

Thanks!
-Brett.


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Re: [O] Indentation messed up after example block

[Brett Viren]

Hi,

Alexander Baier alexander.ba...@mailbox.org writes:

 On 2014-07-06 20:03 York Zhao wrote:
...
 #+BEGIN_EXAMPLE
 * Example at level one
 #+END_EXAMPLE

 Indentation is wrong.

 The asterisk followed by a space followed by text in your example block
 is recognized by org as a headline. So org thinks everything under that
 headline is the body of the headline.

I hit this very problem recently and first assumed it must be a bug.
But, since it's documented[1] I guess it's a feature.  Although one I
don't immediately see a use for.

I hit this when capturing some logging info which happened to have a
line starting with a triple-*.  Trying to manually find such offending
lines in a large EXAMPLE block is too tedious to contemplate.  A better
way, which is implied by that footnote, is to use Org Src buffers when
entering the content of EXAMPLE blocks in the first place.  I do like:

  e TAB C-c' PASTE C-c'

Where PASTE is me pasting or typing whatever is the content of the
EXAMPLE block.

This will not only indent the entire block with a couple of spaces but
will escape the problematic headline asterisk with the special
syntax comma.

-Brett.

[1] http://orgmode.org/manual/Literal-examples.html#fnd-4


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Re: [O] Reverse lookup from pdf to org?

[Brett Viren]

Rainer M Krug rai...@krugs.de writes:

 Brett Viren b...@bnl.gov writes:
   file:///path/to/foo.tex.orglink?line=42

 But jumping to the .org file would be the aim - right?

Yes, right.  Maybe a better example is:

  file://foo.orglink?line=42

which might get interpreted as go to line 42 in ./foo.org.

This example is also a relative link which would be less brittle as long
as foo.org and foo.pdf are kept together in the same directory.

 Chance of success: 10%

 I guess higher?

I like your optimism!

-Brett.


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Re: [O] Reverse lookup from pdf to org?

[Brett Viren]

Rainer M Krug rai...@krugs.de writes:

 Therefore I export the document to pdf, and look for errors there. Now I
 have to find the corresponding section in the org file - possible, but
 tedious.

Not quite what you have in mind and maybe only a half-measure but when I
produce draft latex documents I like to turn on this package:

\usepackage[color]{showkeys}

It prints the symbol used for labels, references and citations in light
gray in the PDF output.  I can then search for these in the tex to find
the corresponding region.  To the extent they are set in your .org
source you might do similar.

A little screen cap is attached to show an example output.


-Brett.

attachment: foo.png

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Re: [O] Reverse lookup from pdf to org?

[Brett Viren]

Nick Dokos ndo...@gmail.com writes:

 One more (half-)possibility is as follows: produce the tex file and
 compile it not with pdflatex, but with plain latex, producing a DVI
 file. Passing the -src option to the latex invocation inserts source
 specials into the DVI file that some DVI viewers (in particular, xdvi)
 can interpret to jump back from the DVI view to the (approximate)
 corresponding location in the tex file:

   latex --shell-escape -src foo.tex
   xdvi foo.dvi

Okay, here is a crazy idea.  Maybe one can use hyperref and place \url{}
and/or \href{}{} macros in the org file.  These will turn into clickable
links in the final PDF.  In them place URLs that look like:

  file:///path/to/foo.tex.orglink?line=42

And then use .mailcap (or whatever MIME config that xpdf/evince/etc
honors) to map the .orglink extension to a script that parses the URL
(does that full URL get passed?) and invokes emacs to open foo.tex at
line 42?

If that much can be made to work (big if!) I see one problem in that the
/path/to will break if the source is moved.

Chance of success: 10%

-Brett.


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Re: [O] Finer-grained control of published files

[Brett Viren]

Bastien b...@gnu.org writes:

 Please test the attached patch against the tip of the master branch
 and let me know if it works: it checks against a .oxignore file, one
 regexp on each line.  If you find it useful, I'll commit this for
 the next version.

I had some unrelated trouble with the head of master so I applied your
patch to the 8.2.5h tag.  It applied cleanly with a little fuzz.

It seems to work great! I played with various ways to ignore and
couldn't make it fail.  

One thing, and I know it's going back on what I asked originally, but I
wonder if file globs would be the more natural pattern matching here
than regexp?  

Either way, this will really help publishing from my messy source
directories  

Thanks!
-Brett.


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[O] Finer-grained control of published files

[Brett Viren]

Hi,

I'm trying to set up org-publish and am looking for more fine-grained
control over what files get published than what (I think) I can get from
configuring org-publish-project-alist.  I've played with the
publishing-function of org-publish-attachment and :exclude/:include and
:base-extension regexps.

What I'm finding is that I want to control what type of files get
published on almost a per-directory basis and different directories may
have mutually conflicting file patterns to include/exclude.  Creating a
new org-publish-project-alist entry for each is tedious.

What I hope for is something equivalent to git's .gitignore
functionality where I can place, say, .orgignore files full of regexp
patterns anywhere in my org source tree and have org-publish honor them.

Is there anything in this direction?

Thanks,
-Brett.




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Re: [O] Graph not hierarchical?

[Brett Viren]

Lawrence Bottorff borg...@gmail.com writes:

 being able to organize and
 extract based on your stuff being stored graph-aware would be nice,
 IMHO. 

I'm by no means an expert on this but I know org-element-parse-buffer
returns a data structure which is a directed-graph.

  http://orgmode.org/worg/org-api/org-element-api.html

Note, each node has a :parent reference which makes the data structure
circular.  Traversing it must take this feature into account.

-Brett.


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Re: [O] terminal emulators

[Brett Viren]

Gregor Zattler telegr...@gmx.net writes:

 Hi Achim,
 * Achim Gratz strom...@nexgo.de [10. Feb. 2014]:
 You cannot enter C-: in some terminals because it would require
 simultaneous processing of shift and control (these terminals ignore
 shift while control is pressed).

 this is true for xterm, rxvt-unicode, gnome-terminal, konsole and
 the linux console.

This terminal feature surprised me so I checked a few terminals I have
here.

xterm on Debian (278-4) does pass the C-:.  Testing with C-c C-: after
starting emacs -nw -q in that xterm I get the expected:

  C-c C-: is undefined

But, I confirm that mate-terminal (1.6.1-1.1+7.wheezy) and rxvt
(1:2.6.4-14) strip off the Ctrl.  There the test produces:

  C-c : is undefined

I note that mate-terminal does process Ctrl+Shift as some of its
shortcuts use this combo.  So, it's actively stripping the Ctrl away.

-Brett.


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Re: [O] most robust linking practices?

[Brett Viren]

Hi John,

John Kitchin jkitc...@andrew.cmu.edu writes:

 The files are all on a unix file system served over nfs, so everyone
 has the same / root. the users (students) have read access to my
 files.

 I am working towards creating packages of notes in org-mode (they
 might even be installed as emacs packages) for the courses that I
 teach. Having relative paths within a package certainly makes sense. I
 would like to link to notes in other packages too, as the courses are
 related, and build on each other. but I won't know in advance where
 those get installed. It sounds like those packages will have to have
 some variables configured to make that work out.

How about defining a slew of links in org-link-abbrev-list.  Say, one
for each set of class notes.

Maybe you'd maintain two copies of such a list, one that assumes your
shared file system is being used and one that assumes some layout
convention in the user's home directory.  Your users could pick the best
one or use them as a starting point for their own customization.

The fact that the link definitions may contain inline lisp functions may
help to organize this.

I guess you would need some way to update your reader/user's copy of the
list as it evolves.  Immediately, I don't have any ideas about that.

I've started to use this approach a little.  So far, just to reference
some common external links.  Here's my setup:

#+BEGIN_SRC elisp
;; Custom external links
;; http://orgmode.org/manual/Adding-hyperlink-types.html#Adding-hyperlink-types
;; http://orgmode.org/manual/Link-abbreviations.html#Link-abbreviations
(defun bv-link-resolve-github (tag)
  (replace-regexp-in-string : /blob/master/ tag))

(setq org-link-abbrev-alist
  '(
(ghsite . https://github.com/brettviren/%h;)
(ghfile . https://github.com/brettviren/%(bv-link-resolve-github))
(dbtrac . http://dayabay.ihep.ac.cn/tracs/dybsvn/ticket/%h;)
))
#+END_SRC

-Brett.


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Re: [O] Parsing Org-mode in Python

[Brett Viren]

Hi Daniel,

Daniel Clemente n142...@gmail.com writes:

   Are there already Python parsers for it?

Parsing generic JSON is fairly trivial in Python.

  import json
  data = json.dumps(open('file.json').read())

The resulting data is then a bunch of Python lists and/or dicts
matching whatever structure was output from org and is in the .json
file.  The schema in these three contexts are (will be) identical.

At this point, Pythonistas can do what they want with data.  Although,
as I mentioned, I'd like to put another layer on this raw data
structure which expresses/enforces the org schema as understood by the
org-exporter.  If I can figure out how to dump a representation of this
schema from org I'll express it as a set of generated
collections.namedtuple instances.  We'll see.

   Should ox-json's output be as raw as possible (e.g. what your code
 produces now) or transformed to simpler JSON?
   (I think both formats should coexist).

I suppose there may be a usefulness to winnow down the structure.  One
thing I'm thinking about here is the narrowing done to support the blog
From anywhere feature of Karl's lazyblorg mentioned in this thread.

That can be done either on the emacs side or Python side (or both, in
principle).  However, my intention is to do as little modification of
the org document structure on the emacs-side in order to preserve
details that may possibly be interesting on the Python-side in the
future.  Also, I'm still learning LISP but know Python fairly well so
would rather do as much processing as possible on the Python side. :)

So far the only thing I see that needs to be stripped is the :parent
property (and the :structure, which really should be resolved as a copy
instead of being stripped) which cause the emacs-side data structure to
become a Circular Object and thus break the emacs JSON dumper.  

I just noticed that Python's JSON dumper can do this kind of stripping
implicitly and in general.  It might be nice if someone were to add such
a feature to the emacs JSON dumper but I don't plan to try this.

-Brett.



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Re: [O] working on cloud

[Brett Viren]

David Belohrad da...@belohrad.ch writes:

 1) privacy: you're basically giving your data to somebody else. In case
of emacs init there is no danger. In case of your org data, which
might contain sensitive information you want to encrypt it, what
complicates matter when switching between two win/lin machines

An alternative to consider is btsync.  It will provide you similar
functionality as Dropbox but removes reliance on a central server which
is outside your control.  All storage endpoints are peers.  Peers are
authorized by a shared key so only your machines, or maybe your friends
get access - it's not an anonymous p2p system despite the bt in its
name.  You can also allow read-only access.  Even with no well known
server involved I've yet to find a case where peers can not be located
behind firewalls or NAT'ed routers.

Of course, btsync brings it's own issues.  The main one for me is that
it's not Free Software (it is a free-of-charge binary) but then the
server side of Dropbox is even more restricted.  I guess let your own
conscience be the guide here.

Personally, I go the git/github route for .emacs files and a private git
repo for org files.  I would like to not have the (explicit)
commit/push/pull steps for org files and so have been testing btsync.
Ideally there would be some way to marry the benefits of both, but I've
yet to come up with one.

-Brett.


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Re: [O] Parsing Org-mode in Python

[Brett Viren]

François Pinard pin...@iro.umontreal.ca writes:

 Brett Viren b...@bnl.gov writes:

   http://permalink.gmane.org/gmane.emacs.orgmode/79838

 This yields:

 ,
 | Not Found
 | 
 | The requested URL /gmane.emacs.orgmode/79838 was not found on this server.
 `

Huh, maybe a transient failure?  It's there for me right now.  Here is
the same message from GNU's archive:

  http://lists.gnu.org/archive/html/emacs-orgmode/2013-12/msg00415.html

In any case, here is the salient chunk:

#+BEGIN_SRC elisp
  (require 'json)
  (let* ((tree (org-element-parse-buffer 'object nil)))
(org-element-map tree (append org-element-all-elements
org-element-all-objects '(plain-text))
  (lambda (x) 
(if (org-element-property :parent x)
(org-element-put-property x :parent none))
(if (org-element-property :structure x)
(org-element-put-property x :structure none))
))
(write-region
 (json-encode tree) 
  nil foo.dat))
#+END_SRC

This test is meant to run from inside an org-mode buffer which itself
provides the fodder for the test.  But, it shows the steps that I'll
need to integrate into some new org export mechanism.  The important
part is nulling out the :parent and :structure (and maybe others?)
properties in order to break their circular references.  The heavy
lifting is all in org-element-parse-buffer and json-encode.

 At the end of the day one will have a DOM-style data structure
 representing the initial org document.

 Keep me (us!) posted! :-)

Definitely!  
-Brett.


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Re: [O] Parsing Org-mode in Python

[Brett Viren]

Hi Karl,

Karl Voit devn...@karl-voit.at writes:

 Hi!

 * Daniel Clemente n142...@gmail.com wrote:
 
 I dream of having a general Python parser for Org mode files, knowing
 every bit about the current syntax for Org files, surrounded by enough
 Python machinery to make it useful.

 Oh, this would be great since there are way more Python-coders out
 there as ELISP coders.

I agree.

I'm also (slowly) working toward some Python-based org processing.  My
strategy is to produce an intermediate file in JSON format which is
designed to capture the full org document structure.  I am calling this
a shunt export as it is meant to do as little interpretation of the
document as possible.

If this is interesting to you and you haven't already seen it please
check the thread from December were I got a lot of help to output this
JSON via the new org export mechanism (I'm a LISP newbie).  Here is the
concluding post with a working example:

  http://permalink.gmane.org/gmane.emacs.orgmode/79838

Besides any eventual Python-side development, one remaining gap in my
plan is how to produce some kind of schema description using the org
exporter machinery.  I want to have this description generated
automatically so that any future changes to the org format can be
accommodated with some level of automation.

So, my current thinking is to find a way to exploit org export machinery
to generate this schema (call it a meta-shunt export?).  If I can find
that I'll output it as another JSON file.  Then, on the Python-side, I
will read this schema file in and generate instances of
collections.namedtuple.  Finally a reader of the JSON org document will
be developed to produce objects of these namedtuple classes.

At the end of the day one will have a DOM-style data structure
representing the initial org document.

-Brett.


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Re: [O] email - TODO items?

[Brett Viren]

Peter Davis p...@pfdstudio.com writes:

 I use half a dozen email clients, including mutt, which lets me easily
 pipe a message to a script.

The need to support multiple clients may rule out my suggestion but
capturing a TODO or a note while visiting a GNUS message and thus
preserving the link back to the article that spawned my task/idea is
fantastically useful.

In your pipe scheme maybe there is some way you can preserve this link
back.

-Brett.


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Re: [O] Org mode and shunt exporters?

[Brett Viren]

Hi,

Nicolas Goaziou n.goaz...@gmail.com writes:

 You can walk the tree, e.g. with `org-element-map', and remove
 all :parent references if you don't need them.

I figured out how to follow this advice.  I can even make valid JSON
From the filtered parse tree by handing it to Edward O'Conner's
json.el (link in example below).

However this method only works for a very simple org document.  I'm
successfully filtering out the :parent properties of (most of) the
elements but as soon as my document produces a plain text element like:

  #(Text 0 4 (:parent #1))

then two problems occcur:

First, I'm simply failing to see how to set this :parent property to nil
like I do with the others.  

Second, json.el throws a Bad JSON Object error.  I tried assuming that
the problem was it doesn't know what to do with this substring form.
Naively, I tried to follow some other recent advice in another thread
about using substring-no-properties to strip out the meta data from the
plain text elements.  But this apparently is a net no-op as I suspect
that the org-element-set-contents then puts them right back.

I feel like I'm pretty close.  Any more advice?

Thanks,
-Brett.


#+TITLE: The Title.

Blah blah blah.

* A heading.

This uses http://edward.oconnor.cx/2006/03/json.el

 - foo
 - bar
 - baz

#+BEGIN_SRC elisp
  (require 'json)
  (let* ((tree (org-element-parse-buffer 'object nil)))
(org-element-map tree org-element-all-elements 
  (lambda (x) 
(if (org-element-property :parent x)
(org-element-put-property x :parent nil))
;; (if (eq (org-element-type x) 'plain-text)
;; (org-element-set-contents x (substring-no-properties 
;;  (org-element-contents x
))
(write-region
 ;(json-encode tree) 
 (prin1-to-string tree)
  nil foo.txt))
#+END_SRC

#+RESULTS:



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Re: [O] Org mode and shunt exporters?

[Brett Viren]

Matt Price mopto...@gmail.com writes:

 I am pretty ignorant and may have missed a referene o this in the
 thread, but this (very outdated) code is on the emacswiki:

 http://www.emacswiki.org/emacs/org-json.el

Thanks.  My searches didn't find this.  It looks like this is parsing
the org buffer directly and only to the level of headings.  Ultimately I
want to emit JSON to get at the full detailed document structure so this
probably isn't in the direction I want to go.

-Brett.




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Re: [O] Org mode and shunt exporters?

[Brett Viren]

Hi Eric,

Eric Schulte schulte.e...@gmail.com writes:

 This should work in a recent Emacs.

 (require 'json)
 (defun org-as-json-to-file (optional path)
   Export the current Org-mode buffer as JSON to the supplied PATH.
   (interactive Fwrite to file: )
   (let ((tree (org-element-parse-buffer)))
 (org-element-map tree
 (append org-element-all-objects org-element-all-elements)
   (lambda (el) (org-element-put-property el :parent nil)))
 (with-temp-file path
   (insert (json-encode tree)

Thanks.  With this, Nicolas's and all the other input I've got something
working now.  There was still one small issue I found with this last
round.  The :structure property also causes an error inside json.el
like:

  json-encode-key: Bad JSON object key: 105

But, for now, nulling :structure in the same way as :parent let's me
chain org-JSON-Python!  The first elisp code block in the test doc
below works.

Thanks for all the patient help from everyone.  I've learned a lot.

-Brett.


#+TITLE: The Title.
Blah blah blah.
* A heading.
This uses http://edward.oconnor.cx/2006/03/json.el
 - foo
 - bar
 - baz
#+BEGIN_SRC elisp
  (require 'json)
  (let* ((tree (org-element-parse-buffer 'object nil)))
(org-element-map tree (append org-element-all-elements
org-element-all-objects '(plain-text))
  (lambda (x) 
(if (org-element-property :parent x)
(org-element-put-property x :parent none))
(if (org-element-property :structure x)
(org-element-put-property x :structure none))
;; (if (eq (org-element-type x) 'plain-text)
;; (org-element-set-contents x (substring-no-properties 
;;  (org-element-contents x
))
(write-region
 (json-encode tree) 
 ;(prin1-to-string tree)
  nil foo.dat))
#+END_SRC

#+RESULTS:

* From Eric Schultz
#+BEGIN_SRC elisp
  (require 'json)
  (defun org-as-json-to-file (optional path)
Export the current Org-mode buffer as JSON to the supplied PATH.
(interactive Fwrite to file: )
(let ((tree (org-element-parse-buffer)))
  (org-element-map tree
  (append org-element-all-objects org-element-all-elements)
(lambda (el) (org-element-put-property el :parent none)))
  (with-temp-file path
(insert (json-encode tree)
  (org-as-json-to-file eric.txt)
#+END_SRC

* Try some hand written data
#+BEGIN_SRC elisp
  (require 'json)
  (with-current-buffer (find-file-noselect foo.dat)
(let ((tree (read (current-buffer
  (prin1-to-string (json-encode tree
#+END_SRC



 


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Re: [O] Org mode and shunt exporters?

[Brett Viren]

Hi John,

John Kitchin jkitc...@andrew.cmu.edu writes:

 that sounds like an interesting approach. xml seems like what you
 really want, since looking at the parsetree there is a lot of
 information (e.g. attributes, properties, etc...) that would be tricky
 to generate a fully representative json scheme. 

I see from your other thread that you are looking in to this idea of
dumping to JSON.  That's great!  If you want a tester of your JSON
exporter I'd be very happy to give it a try.  If it means I can abandon
my own stumbling around, that would make me even happier.

But, I am still slowly messing with this myself.  I plan to next follow
Nicolas's suggestion of simply removing the :parent parameter to get
over the hurdle that the circular object caused me.  I think if the
overall structure of the parse tree is preserved in the JSON then
parentage can be restored when it is read back.

I've also thought a bit about schema issues.  Regardless of how an org
schema might be represented, it would be best if it could be generated
From org instead of hand crafted.  This would need a kind of a meta
export feature.  I've not yet checked to see if there is some facility
in org to exploit to do this.  Maybe someone knows?

In the past I've expressed schema descriptions for JSON data in JSON
itself.  Internet searches now show this is not a novel approach so I
think there is some fruit to be found pursuing this direction.  Or, I
may just be trying too hard to avoid XML

 This page suggests at the bottom you could export to texinfo, and
 convert that to docbook:
 http://orgmode.org/worg/exporters/ox-overview.html

 * (1) DocBook export, available in previous Org-mode versions, has not
   currently been ported to the new exporter, however the new
   ox-texinfo backend can generate DocBook format. Once file.texi is
   created via ox-texinfo, simply execute: 

 makeinfo --docbook file.texi

Thanks.  I did try this but makeinfo failed on the texinfo file that was
produced.  I didn't pursue it enough to figure out why or if I was doing
something wrong.

-Brett.


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Re: [O] Org mode and shunt exporters?

[Brett Viren]

Eric Schulte schulte.e...@gmail.com writes:

 You can use `org-element-parse-buffer' to convert an Emacs Buffer to a
 structured Emacs Lisp object.  At that point you can use existing tools
 for converting lisp to JSON or YAML.  I've used cl-json for Common Lisp,
 I would imagine something similar exists for Emacs Lisp.

Thanks for the suggestion.  I pursued that a bit this weekend.  The
resulting data structure is a Circular Object[1] due to the :parent
references.  It seems dealing with this kind of data structure is
somewhat uncommon (or my search-fu lacking), although I do find a recent
reference to it on this mailing list[2].  I also found a cust-print[3]
feature from Emacs 19 which has since been removed.  It shows a way to
deal with Circular Objects.  So far it has strongly taxed my poor elisp
skills but I plan to pursue this direction a bit more.

I did try throwing a JSON parser/generator[4] at the output of
org-element-parse-buffer but this failed due to exceeding emacs's
recursion limits.  I think this must be from the :parent references
getting recursed on forever.


-Brett.


[1] one must (setq print-circle t) to avoid emacs reader errors
http://www.gnu.org/software/emacs/manual/html_node/elisp/Circular-Objects.html

[2] http://comments.gmane.org/gmane.emacs.orgmode/65999

[3] http://web.mit.edu/dosathena/sandbox/emacs-19.28/lisp/cust-print.el

[4] http://edward.oconnor.cx/2006/03/json.el


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[O] Org mode and shunt exporters?

[Brett Viren]

Has anyone written any new-style exporter which will produce a common
markup/data language format like JSON or YAML?  I'm looking for
something that fully preserves the original org document structure and
does no semantic interpretation along the way.

What I really want is to parse arbitrary org files in Python.  I've
looked at the entries at worg's org-tool node which do this but they
seem out of date or make assumptions about what org elements exist or
their URLs are not loading (NEO).  If any of that's a misrepresentation
please correct me.

In any case, using org's own exporter to produce JSON or YAML and then
relying on these format's Python modules for parsing seems like the best
way to go to let me author in org and process in Python.

I'm not very good with elisp (which is why I want to get org data into
Python) but I guess I can have a go at making such a shunt exporter.
Before I try, I just wanted to check if someone had this wheel already
spinning.

Thanks,
-Brett.


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Re: [O] Capture templates with function type

[Brett Viren]

Bastien b...@gnu.org writes:

 Capture templates using `function' should now return back to the
 correct window location.  Thanks for raising this,

Thanks so much for putting time in it!

Regards,
-Brett.


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Re: [O] Capture templates with function type

[Brett Viren]

Hi Bastien,

Bastien b...@gnu.org writes:

 You may try this (not tested myself):

 (defun bv-daily-log-file ()
   (save-window-excursion
 (find-file (concat ~/org/web/notes/ 
  (format-time-string %Y-%m-%d) .org))
 (goto-char (point-max))
 (newline 2)))

 The trick is to use `save-window-excursion'.

Thanks for the pointer but it looks like this macro runs afoul of the
capture process somehow.  I redefined my function as you have above and
did C-xC-e to reload it and then initiated a capture from a window
showing my GNUS summary.  It fails with:

byte-code: Capture abort: (buffer-read-only #killed buffer)

I then tried another capture staring from a read-write buffer.  The
capture succeeds but the captured text is inserted into this starting
buffer instead of the one found by the bv-daily-log-file function.

The Elisp manual mentions that save-selected-window is sometimes a
better alternative but that gives the same behavior.  

Do you maybe have further ideas I could try?  

Thanks,
-Brett.


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[O] Capture templates with function type

[Brett Viren]

Hi,

I'm trying to set up a capture template of type function in order to
produce a daily log file named after today's date.

It mostly works.  However, after doing the C-cC-c to close the capture
buffer the window is left holding the daily log file which the capture
just updated instead of going back to whatever buffer I was in when I
initiated the capture.  This returning-to-previous-buffer behavior is
what I see when I use the file+headline capture type.

Can someone say how I might get this behavior for the function capture
type as well?  Here is my setup:

(defun bv-daily-log-file ()
  (find-file (concat ~/org/web/notes/ 
  (format-time-string %Y-%m-%d) .org))
  (goto-char (point-max))
  (newline 2)
)
(setq org-capture-templates 
 (quote 
  (
   (n Note entry
(function bv-daily-log-file)
\* %U %^{title}\n  %a\n\n%?
:empty-lines 1)
   )))


Thanks,
-Brett.


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[O] Export org to dot for an organization chart?

[Brett Viren]

Hi,

I'd like to produce an organization chart using org.  What I want to do
is:

 - enter an organization role as a section heading
 - have the heading hierarchy map to the organization hierarchy
 - enter optional section properties to specify:
   - the name of the individual who might fill the role
   - color and line types for drawing the box for the role
   - a URL associated with the role
 - section text providing a brief description of the role
 - render this into some nice looking graphic

The end result I'm going for is a clickable image on a web page made by
rendering the organization chart such that clicking on a box sends the
browser to the role-specific URL and the alt text for that link gives
the section text.

Is there already something along these lines?  Some searches turned up
empty

My thinking is that if there was an org-export-as-dot then it would be
close to what I want.

I found org-export-as-freemind which is in the right direction but I
think lacks some of what I want and I'd like to avoid using a GUI in the
process.

Thanks for any ideas on this.  If there is nothing like this yet, maybe
I can use it as an excuse to learn org's new export system.


-Brett.


PS: rough example org file might look like:

* Boss
:PROPERTIES:
:Actor: Bob Bigbooty
:URL: http://www.example.com/boss.html
:NodeColor: blue
:END:

The boss dictates.

** Middle Manager 
:PROPERTIES:
:Actor: 
:URL: http://www.example.com/layer.html
:NodeColor: red
:END:

The middle manager spectates.

*** Flunky
:PROPERTIES:
:Actor: Sam Small
:URL: http://www.example.com/hardworker.html
:END:

While the flunky gets stuff done.


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Re: [O] Amazing demonstration by John Kitchin

[Brett Viren]

John, I finally got a chance to watch your really nice SciPy talk last
night.

I've been trying to incorporate Reproducible Research methods with org
into my own work.  I strive to do more and what you are doing looks to
provide a wealth of examples.  I hope more researchers follow this
methodology.

One thing I've yet to get a good handle on is publishing org content in
an automated (and beautiful) way.  I was very taken with your github.io
pages and would like to try to set up something similar for myself.

Do you have a write-up or other guidance on this that I might follow?
I've started to go through your related github repositories to figure
out what you do but if something more guided exists it would help.

Thanks,
-Brett.

Carsten Dominik carsten.domi...@gmail.com writes:

 Hi,

 I don't know if this has been linked to before on this mailing
 list.  At SciPy 2013, John Kitchin has made an amazing
 demonstration of Org-mode as a tool for reproducible research.
 Really amazing to watch.

 http://www.youtube.com/watch?v=1-dUkyn_fZA

 - Carsten


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Re: [O] Amazing demonstration by John Kitchin

[Brett Viren]

John Kitchin jkitc...@andrew.cmu.edu writes:

 Here is part of how I use org-mode to publish to my blog:
 http://jkitchin.github.io/blog/2013/09/27/Publishing-to-blogofile-using-org-mode/

Thank you very much for typing this up!  I now have some weekend
entertainment to try and replicate it for myself.

-Brett.


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Re: [O] Org mode issue tracker

[Brett Viren]

Hi,

Suvayu Ali fatkasuvayu+li...@gmail.com writes:

   * TODO Subject timestamp :emacs_ver:org_ver:org_module:
...
 Emacs version ends up as a tag:

 * TODO  .   :24.3:

Or, if I add an Org version:

 * TODO  .   :24.3:8.0.3:

These bare numbers seem a bit too anonymous to me.  I think it's
unlikely that Org will reach versions in the 20's anytime soon so
collision won't happen for a while but eventually (hackers willing!) it
will.

So, I suggest simply qualifying the versions like:

  * TODO  .  :emacs_24.3:org_8.0.3:

I can also see a desire to list other software and their versions that
might be implicated in the bug being reported.  Listing their bare
versions as tags is, I think, obviously no good.  They could just
include this info in an ad-hoc manner in the body of their report, but
maybe it would be good to define a property to explicitly list them
following the same package_version pattern of the tags.

  * TODO  .  :emacs_24.3:org_8.0.3:
:PROPERTIES:
:IMPLICATED_SOFTWARE: texlive_2012.20120611-5 beamer_3.10-2


BTW, I think an issue tracker in Org is very interesting.  I look
forward to seeing how it evolves.

-Brett.


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Re: [O] asynchronous code evaluation

[Brett Viren]

Hi Johannes,

Johannes Rainer johannes.rai...@i-med.ac.at writes:

 well, I'm using emacs/org for my data analyses in R. I thus combine
 documentation (i.e. the conclusions drawn from e.g. plots created in
 R) and the R code to perform the analysis in my org file. Since I'm
 analysing high throughput data some tasks to handle the data are quite
 time consuming.

A variation on Allen's Makefile approach, I structure my (Python) code
to be idempotent.  The real code never (re)runs unless its output
either doesn't exist or is older than the input.  Normally when org runs
the code's higher level interface it's essentially a no-op and very
fast.  If something does change it's usually because I'm doing
development and will be running the code outside of org enough that it's
reached its no-op state before I go back into emacs to refresh/edit
the org document.  Also, I keep things synchronous to avoid having to
multiple, competing processes running at once.

What I want is to take this approach and generalize into a more formal
workflow system.  One which handles caching files and in-memory objects
in a versioned store to provide data provenance and idempotent running
in a general sense.  There's already been some work on this (bein,
pyutilib workflow and sumatra to name some Python oriented ones) but
so far nothing that just fits.  I'm in the middle of trying my hand at
something better, but it's not yet usable.

-Brett.


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Re: [O] org-export-current-backend variable and org-mode 8

[Brett Viren]

Hi Christophe,

Christophe Rhodes cs...@cantab.net writes:

 In org-mode 7, I was able to use the (documented) variable
 org-export-current-backend to test what the current backend is, allowing
 me to dynamically produce and include images of different formats
 depending on whether I was exporting to latex (tikz) or html (png).

 In org-mode 8, I cannot find this variable, or any documented variable
 of a similar nature.  What is the recommended way for dispatching at the
 emacs-lisp level when exporting a document on the export backend?

I don't know if this is exactly what you are asking for but I hit on the
following a few weeks ago.  It defines an elisp macro inside the org
file and then calls it later in the header of a code block to switch the
output file names based on which backend (if any) is in effect.  I hope
it helps.

If you have a better way to do these kind of output switches, I'd like
to know.


* COMMENT setup

#+begin_src emacs-lisp :results silent
  (defmacro by-backend (rest body)
`(case (if (boundp 'backend) backend nil) ,@body))
#+end_src
  
* A graph

#+header: :file (by-backend (html graph.png) (latex graph.pdf) (t 
graph.svg))
#+header: :export results
#+begin_src dot
digraph Name {
tail - head;
}
#+end_src


-Brett.


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[O] Interpreter/shell prompts when exporting code blocks?

[Brett Viren]

Hi organistas.

I'd like to have my executable code blocks get exported to HTML/LaTeX
with some prompt prefixed to each line of code but still let the blocks
themselves remain executable in their given language.  Is there already
a nice way to do this?

For example, if there was something like a prompt header to specify
what should get prefixed on export then something like...

#+prompt: $ 
#+BEGIN_SRC sh :results none :exports code
mkdir mymod
touch mymod/__init__.py
#+END_SRC

#+prompt:  :indent ...
#+BEGIN_SRC python :results none :exports code
import mymod
def myfun():
mymod.something()
#+END_SRC

...would export something resembling:

$ mkdir mymod
$ touch mymod/__init__.py

 import mymod
 def myfun():
... mymod.something()


For HTML export, some stylesheet magic which allows any cut-and-paste to
ignore the prefixed prompt would be icing on an already tasty cake.

-Brett.


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[O] Switch for exported file types when evaluating code blocks

[Brett Viren]

Hi,

I'm hitting on an old theme in a new way here.  

I want graphics files which are exported by evaluated code blocks to be
generated in a format best suited to their intended use.  For HTML I
want either PNG or SVG.  For LaTeX/PDF I almost always want PDF.  For
inline viewing in emacs I want either PNG or SVG.

To that end I went a'googling and found this idea:

  http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html#sec-4-3

It doesn't work with my copies[1] of emacs and org-mode but I was able
to adapt it.  I suck at elisp so this is probably more an accomplishment
to me than it appears to most of you!

In any case, here is a short org document based on the one I found above
in worg which shows what I ended up with:


* COMMENT setup
#+begin_src emacs-lisp :results silent
  (defmacro by-backend (rest body)
`(case (if (boundp 'backend) backend nil) ,@body))
#+end_src

* A graph
#+header: :file (by-backend (html graph.png) (latex graph.pdf) (t 
graph.svg))
#+header: :export results
#+begin_src dot
digraph Name {
tail - head;
}
#+end_src


I think the real learning experience for me was that I could put lisp
directly in a header like this!  Now, I just gotta learn elisp
better

Also, I'd certainly be interested to hear of any better ways to
accomplish this.

Thanks,
-Brett.


[1] The versions I'm using are

 - Org-mode version 8.0.3 (8.0.3-elpa @ 
/home/bviren/.emacs.d/elpa/org-20130514/)

 - GNU Emacs 24.1.1 (i486-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-07-20 on 
murphy, modified by Debian


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Re: [O] advice needed: how do you guys sync org files between devices?

[Brett Viren]

Alan Schmitt alan.schm...@polytechnique.org writes:

 Well, what would be there? If there is (and there may be) an external
 tool that knows how to merge org files (it can be a 3-way merge, if it
 makes things simpler), I could try to devise the magical incantation to
 use it.

It is not org-specific, but meld [1] is a Free and capable GUI merge
tool.  It can be used directly or can be invoked by git to resolve merge
conflicts.


-Brett.

http://meldmerge.org/


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Re: [O] RFQ - new contribution - org-screenshot.el

[Brett Viren]

Hi Max, 

Max Mikhanosha m...@openchat.com writes:

 I have committed org-screenshot to master

This sounds like a great idea.  And just to prove that no good deed goes
unpunished, here is a bug report:

In an org-mode file I run M-x org-screenshot-take, scrot runs and I
can either click on a window or draw a selection box.  

However, lifting the mouse button leads to:

  error in process sentinel: Symbol's value as variable is void: return [2 
times]

An actual PNG is produced in the expected images/ subdir and also I
confirm that running /usr/bin/scrot -s /path/to/file.png by hand works
returning a 0 error code.

My org is:

  Org-mode version 8.0.3 (8.0.3-elpa @ /home/bviren/.emacs.d/elpa/org-20130514/)

Running in:

  GNU Emacs 24.1.1 (i486-pc-linux-gnu, GTK+ Version 2.24.10) of 2012-07-20 on 
murphy, modified by Debian

I copied the org-screenshot.el you just pushed from git's contrib/ to my
load path and added a (require 'org-screenshot) just after my
(require 'org).  The same behavior also occurs with the original copy
you posted to this mailing list.

A quick Google search just left me confused (I'm not great with elisp).
Is there anything I can do to debug this further?

Thanks,
-Brett.


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[O] Nested list with percent-complete in multiple states?

[Brett Viren]

Hi,

I'm helping to edit a large document with section contributions from
many people.  Any given section may come in some bizarre format (ie,
.doc) which I convert to LaTeX, leave open a time for subsequent edits
and finally freeze the section.

I'd like to track this state using org-mode.

So far I've been using a nested checklist like:

* Document Sections [0/4]
  - [-] Chapter 1 [0/3]
- [ ] section 1 (person A)
- [ ] section 2 (person B)
- [ ] section 2 (person C)
  - [-] Chapter 2 [1/1]
- [X] section 1 (Person D)

This is okay for binary state, but is there any to have more states
represented and get a summary of the percent of each chapter/section in
that state?

For example, I'd like something like:

* Document Sections (received:[1/4] converted:[1/4] frozen:[1/4] missing [1/4])
  - [-] Chapter 1 (received:[2/3] converted:[1/3] frozen:[0/3] missing [1/3])
- [ ] section 1 (person A)
- [R] section 2 (person B)
- [C] section 2 (person C)
  - [-] Chapter 2 (received:[1/1] converted:[1/1] frozen:[1/1] missing [0/1])
- [F] section 1 (Person D)


Is there anything which gets me in this direction?

Thanks,
-Brett.


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Re: [O] Nested list with percent-complete in multiple states?

[Brett Viren]

Bastien b...@gnu.org writes:

 Check boxes have only three state: empty, checked, undecided.

 If you need more states, I suggest using a property.
 Then the column view can be used to display a summary
 of the sum of all properties in the subtree.

Thanks for the pointer, Bastien.  This looks like a fine way to do
things.  

I've been able to capture the columnview into another .org file and
then export that to an HTML file.  Is there a way to automate these
three steps?


Notes on what I did so far follow.

In a notes.org:

* Document status
 :PROPERTIES:
 :COLUMNS: %25ITEM(Section) %25Responsible %3Received{X} %3Converted{X} 
%3Editing{X} %3Frozen{X}
 :Responsible_ALL: Person1 Person2 Person3
 :Received_ALL: [ ] [X]
 :Converted_ALL: [ ] [X]
 :Editing_ALL: [ ] [X]
 :Frozen_ALL: [ ] [X]
 :ID:   document-status
 :END:   

** Section 1
*** Subsection 1.1
 :PROPERTIES:
 :Responsible: Person1
 :Received: [X]
 :Converted: [ ]
 :END:


Etc for other sections.  Hints:

 - only need to add properties in sub (or subsub, etc) sections where
   they are strictly needed.  Parents inherit from children

 - don't actually edit :PROPERTIES: by hand instead do C-c C-x C-c to
   turn on columns and e in a cell to edit it with values from the
   list of possible ones in the *_ALL and/or do C-c C-c to toggle values

I shall look into adding numerical values to get %-done type columns.

Then for presentation.  As per

  http://orgmode.org/manual/Capturing-column-view.html

To make presentation with just this tree of info make another file
status.org with:

* Status
#+BEGIN: columnview :vlines t :hlines 1 :id document-status
#+END:

Go to BEGIN and hit C-c C-c and a table will be inserted.  Then a
normal export to HTML can be done.   


-Brett.



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Re: [O] The statement on what is orgmode.

[Brett Viren]

Rasmus ras...@gmx.us writes:

 Orgmode: your life, in plain text.

 I like the idea of a catch phrase (your life, in plain text) and
 perhaps a more detailed paragraph belows, potentially with links.

This phrase is also what first comes to my mind when I try to explain
org-mode to others.

However, it is clear there are many apt description-blurbs.  How about
having a database along the lines of what people are saying about
org-mode that is initially seeded with what has come up in this thread
and then have each refresh of the main org page select and present a new
one?  I'm sure there are lots of issues and details with this idea so I
just toss it out there.

-Brett.


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Re: [O] How to integrate org-mode in a MS Windows-/Office-based environment?

[Brett Viren]

Hi Martin,

M elwood...@web.de writes:

 One example of helpful integration: if I send or get an e-mail which I want
 to follow-up on later, I want to track that in org-mode and I want to have a
 way to quickly find the original message in Outlook again (to reply or
 forward it or whatever), which can be done with hyperlinks.

You can simplify making links to your email messages by creating a
custom link abbreviation assuming there is some uniquely identifying
chunk of the URL to use as a key.

Here are examples using google search and maps:

;; in .emacs
(setq org-link-abbrev-alist
  '(
(google   . http://www.google.com/search?q=;)
(gmap . http://maps.google.com/maps?q=%s;)
))

Example org markup:

[[google:org-mode][org-mode on google]]



-Brett.


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[O] Multiple images per figure with LaTeX export

[Brett Viren]

I'm using GNU emacs 23.2+1-7 and org-mode 6.27a-1 on Debian.

I want to put two images in one figure for LaTeX/PDF export but can't
find a way.  Googling has not born fruit.  I have tried a few naive
things like:

#+caption: Caption.
#+label: fig:figure
[[./img1.pdf]][[./img2.pdf]]

or:

#+caption: Caption.
#+label: fig:figure
[[./img1.pdf]]
[[./img2.pdf]]

but the resulting export has either two figures with identical captions,
each holding one of the images or the first image in a figure and the
second image inserted bare.  I've also tried to put each image in the
cell of a table but that leads to an undefined control sequence error.

How can this be done?

Thanks,
-Brett.


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Re: [O] Multiple images per figure with LaTeX export

[Brett Viren]

Hi Suvayu,

suvayu ali fatkasuvayu+li...@gmail.com writes:

 Glad to see another HEP researcher using org-mode. :)

Greetings!

 Sadly my solution is a big bad hack:

   #+begin_latex
 \begin{figure}
 \centering
 \begin{tabular}{c}
 \includegraphics[options]{plots/file1.eps} \\
 \includegraphics[options]{plots/file2.eps}
 \end{tabular}
 \caption[Caption in LOI]{Long caption}
 \label{fig:somelabel}
 \end{figure}
   #+end_latex

Okay, thanks!  I didn't think about just putting it directly in LaTeX.
This will works just fine for my purposes.

Cheers,
-Brett.


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Re: [O] python/babel inline images

[Brett Viren]

henry atting nsmp...@online.de writes:

 I do not succeed in generating an inline image as a result of a
 python code block. The code itself works, C-c C-c generates the
 according picture, but only in my home directory. The code block:

Could you not just follow the block with a hand-written link to the
output file?  Then, when it becomes available toggle C-c C-x C-v (once
or twice) or M-x org-display-inline-images once.

Maybe also rewrite the Python to place the output SVG in a directory
associated with your ORG file so that link can be relative.  I simply
use an env. var. to locate where my plots should output.

I'm an org-newbie so maybe there are better ways.

-Brett.


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[O] Embed images in formats best suited for HTML and LaTeX export and inline viewing

[Brett Viren]

Hi,

How can I tell org-mode to use different file formats for an image for
different purposes?

What I really want is a scalable format to embed line art type images
(plots) into org-mode documents so that they can display inline and in
both HTML and LaTeX exports.  SVG seems good for the first two but LaTeX
doesn't accept it.  Likewise, LaTeX wants PDF but inline and HTML export
do not.

Anyway to eat my cake?

Thanks,
-Brett.


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