[BABEL] Redirect stderr to stdout?

[BABEL] Redirect stderr to stdout?

[Viktor Rosenfeld]

Hi,

is there a way to capture stderr output of a babel block and have it
appear in the results block (instead of being printed in the *Shell
Command Output* buffer)? On sh blocks I could redirect myself, but I'm
trying to capture the output of psql (the PostgreSQL client).

Specifically, I have the following code block:

#+BEGIN_SRC sql :noweb yes :results output verbatim
\timing on
<<exp8-test-query>>
#+END_SRC

#+RESULTS:
: count
: 95977

The \timing directive causes psql to print the runtime of the query on
stderr. If I run the query on the psql command line, the following
output appears:

 count 
 -------
 95977
 (1 row)

 Time: 1895,558 ms

I suppose that duplicating this output in Babel would be difficult,
because it interferes with the parsing of the result set.

Cheers,
Viktor

Re: [BABEL] Redirect stderr to stdout?

[Eric Schulte]

Viktor Rosenfeld <listuser36@googlemail.com> writes:

> Hi,
>
> is there a way to capture stderr output of a babel block and have it
> appear in the results block (instead of being printed in the *Shell
> Command Output* buffer)? On sh blocks I could redirect myself, but I'm
> trying to capture the output of psql (the PostgreSQL client).
>
> Specifically, I have the following code block:
>
> #+BEGIN_SRC sql :noweb yes :results output verbatim
> \timing on
> <<exp8-test-query>>
> #+END_SRC
>
> #+RESULTS:
> : count
> : 95977
>
> The \timing directive causes psql to print the runtime of the query on
> stderr. If I run the query on the psql command line, the following
> output appears:
>
>  count 
>  -------
>  95977
>  (1 row)
>
>  Time: 1895,558 ms
>
> I suppose that duplicating this output in Babel would be difficult,
> because it interferes with the parsing of the result set.
>

Hi Viktor,

Currently the only action Babel takes with STDERR is to display it in a
pop-up buffer when code block evaluation fails.  It would certainly be
possible to add :results header argument to incorporate STDERR into
results (and this desire has been expressed previously).  Reasonable
combination options would likely include (at least) the following.

| stderr-only | return stderr instead of stdout    |
| 2>&1        | interleave stderr and stdout       |
| concat      | add stderr to the end of stdout    |
| list        | return a list of stderr and stdotu |

The best (read simple and extensible) implementation and syntax for this
behavior is not obvious to me (and I simply don't have time).  If you
(or anyone on the list) have any interest in hacking elisp code the
place to start would be `org-babel-eval' for a serious implementation,
or an quick hack may be possible through customization of the
`org-babel-eval-error-notify' function.

Hope this helps.

Best,

>
> Cheers,
> Viktor
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [BABEL] Redirect stderr to stdout?

[Viktor Rosenfeld]

Hi Eric,

Eric Schulte wrote:

> Currently the only action Babel takes with STDERR is to display it in a
> pop-up buffer when code block evaluation fails.  

On my system (OS X) the buffer does not popup. I just tried

#+BEGIN_SRC sh
echo foo 1>&2
#+END_SRC

in Aquamacs and Cocoa Emacs. Strangely, the output seems to be lost
entirely. Normally, stderr is captured in another buffer which I have to
open manually.

> It would certainly be
> possible to add :results header argument to incorporate STDERR into
> results (and this desire has been expressed previously).  Reasonable
> combination options would likely include (at least) the following.
> 
> | stderr-only | return stderr instead of stdout    |
> | 2>&1        | interleave stderr and stdout       |
> | concat      | add stderr to the end of stdout    |
> | list        | return a list of stderr and stdotu |
> 
> The best (read simple and extensible) implementation and syntax for this
> behavior is not obvious to me (and I simply don't have time).  If you
> (or anyone on the list) have any interest in hacking elisp code the
> place to start would be `org-babel-eval' for a serious implementation,
> or an quick hack may be possible through customization of the
> `org-babel-eval-error-notify' function.
> 
> Hope this helps.

Okay, thanks. My elisp skills are very rudimentary and this is beyond
me. Maybe somebody else will pick it up if the interest is big enough.

Cheers,
Viktor

Re: [BABEL] Redirect stderr to stdout?

[Eric Schulte]

Viktor Rosenfeld <listuser36@googlemail.com> writes:

> Hi Eric,
>
> Eric Schulte wrote:
>
>> Currently the only action Babel takes with STDERR is to display it in a
>> pop-up buffer when code block evaluation fails.  
>
> On my system (OS X) the buffer does not popup. I just tried
>
> #+BEGIN_SRC sh
> echo foo 1>&2
> #+END_SRC
>

That is because the evaluation did not fail, try

#+BEGIN_SRC sh
echo foo 1>&2
exit 1
#+END_SRC

>
> in Aquamacs and Cocoa Emacs. Strangely, the output seems to be lost
> entirely.

I don't pretend to understand the many oddities of Aquamacs, and I don't
know what Cocoa Emacs is.

> Normally, stderr is captured in another buffer which I have to open
> manually.
>
>> It would certainly be
>> possible to add :results header argument to incorporate STDERR into
>> results (and this desire has been expressed previously).  Reasonable
>> combination options would likely include (at least) the following.
>> 
>> | stderr-only | return stderr instead of stdout    |
>> | 2>&1        | interleave stderr and stdout       |
>> | concat      | add stderr to the end of stdout    |
>> | list        | return a list of stderr and stdotu |
>> 
>> The best (read simple and extensible) implementation and syntax for this
>> behavior is not obvious to me (and I simply don't have time).  If you
>> (or anyone on the list) have any interest in hacking elisp code the
>> place to start would be `org-babel-eval' for a serious implementation,
>> or an quick hack may be possible through customization of the
>> `org-babel-eval-error-notify' function.
>> 
>> Hope this helps.
>
> Okay, thanks. My elisp skills are very rudimentary and this is beyond
> me. Maybe somebody else will pick it up if the interest is big enough.
>

This feature has been requested previously on the mailing list, so there
is certainly demand.  As always demand outstrips development resources.

Best,

>
> Cheers,
> Viktor
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: [BABEL] Redirect stderr to stdout?

[Viktor Rosenfeld]

Hi Eric,

Eric Schulte wrote:

> Viktor Rosenfeld <listuser36@googlemail.com> writes:
> 
> > Hi Eric,
> >
> > Eric Schulte wrote:
> >
> >> Currently the only action Babel takes with STDERR is to display it in a
> >> pop-up buffer when code block evaluation fails.  
> >
> > On my system (OS X) the buffer does not popup. I just tried
> >
> > #+BEGIN_SRC sh
> > echo foo 1>&2
> > #+END_SRC
> >
> 
> That is because the evaluation did not fail, try
> 
> #+BEGIN_SRC sh
> echo foo 1>&2
> exit 1
> #+END_SRC

Thanks, that did the trick. It also explains why some error output from
psql and the like does not make it into the buffer.

> [Snip]
> 
> As always demand outstrips development resources.

And still, org-mode is great product!

Cheers,
Viktor