* org alters output of bash code blocks when run with :session
@ 2018-02-21 22:10 Tyler Smith
2018-02-26 10:27 ` Nicolas Goaziou
0 siblings, 1 reply; 4+ messages in thread
From: Tyler Smith @ 2018-02-21 22:10 UTC (permalink / raw)
To: Emacs Org-Mode Help
Hi,
(originally posted to emacs.stackexchange[1] with no answers, )
I am running a short bash command from an org mode code block, using the program `fold` to wrap it at 60 characters. If I run the code without a session argument, the results display as expected. However, when I set the session argument (which I have to do in the context of the long literate analysis I'm doing), some of the output characters don't appear.
Steps to reproduce:
emacs -Q
Open the following file and execute each code block in turn:
+------------------------
#+BEGIN_SRC elisp setup
(org-babel-do-load-languages
'org-babel-load-languages
'((shell . t)))
#+END_SRC
#+RESULTS:
#+BEGIN_SRC bash no session :results replace verbatim
echo 'CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFDGGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7' | fold -w 60
#+END_SRC
#+RESULTS:
: CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
: GGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFD
: GGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGE
: GC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7
#+BEGIN_SRC bash session :results replace verbatim :session my-session
echo 'CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFDGGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7' | fold -w 60
#+END_SRC
#+RESULTS:
: CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
: GGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFD
: FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGE
: 5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7
+------------------------
Notice the difference between the two bash results blocks. In the first, the input string is folded at column 60, without any other changes. In the second, a string of characters has been deleted:
- `GGGFCF:,FF9>` from the beginning of the third line
- `GC5>` from the beginning of the fourth line
The fact that the deleted strings both start at the beginning of a line and end with a `>` suggests that the session thinks they should be redirected somehow, and in the process is dropping them completely. However, when I look at the session buffer, the output appears as expected, with no missing characters.
How do I force the babel session to leave the output alone, and print it verbatim into the org file?
Thanks!
Tyler
GNU Emacs 26.0.90
Org mode version 9.1.4
[1] https://emacs.stackexchange.com/questions/38964/org-alters-output-of-bash-code-blocks-when-run-with-session
--
plantarum.ca
^ permalink raw reply [flat|nested] 4+ messages in thread* Re: org alters output of bash code blocks when run with :session
2018-02-21 22:10 org alters output of bash code blocks when run with :session Tyler Smith
@ 2018-02-26 10:27 ` Nicolas Goaziou
2018-03-13 17:24 ` Tyler Smith
0 siblings, 1 reply; 4+ messages in thread
From: Nicolas Goaziou @ 2018-02-26 10:27 UTC (permalink / raw)
To: Tyler Smith; +Cc: Emacs Org-Mode Help
Hello,
Tyler Smith <tyler@plantarum.ca> writes:
> I am running a short bash command from an org mode code block, using
> the program `fold` to wrap it at 60 characters. If I run the code
> without a session argument, the results display as expected. However,
> when I set the session argument (which I have to do in the context of
> the long literate analysis I'm doing), some of the output characters
> don't appear.
>
> Steps to reproduce:
>
> emacs -Q
>
> Open the following file and execute each code block in turn:
>
> +------------------------
>
> #+BEGIN_SRC elisp setup
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((shell . t)))
> #+END_SRC
>
>
> #+RESULTS:
>
>
> #+BEGIN_SRC bash no session :results replace verbatim
> echo 'CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFDGGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7' | fold -w 60
> #+END_SRC
>
>
> #+RESULTS:
> : CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
> : GGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFD
> : GGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGE
> : GC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7
>
>
> #+BEGIN_SRC bash session :results replace verbatim :session my-session
> echo 'CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFDGGGFCF:,FF9>FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGEGC5>5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7' | fold -w 60
> #+END_SRC
>
>
> #+RESULTS:
> : CCCC8,,CEFGDF,,,CC,CF:,,C8CFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
> : GGGGGGCFGGGG@GGGGGGGGGGGGGGGGGGGGGGGGGGGGG+FF:B3CDFGGGFGGCFD
> : FEC,F<FEG*?FFFFFGGG*CFEEECGGGGC+>FDGGDGFDFFEEFGE
> : 5?C*CGGF+3:*<7*2>+*<9CGCD::C=*@DCFCFFGG<C9<)7*9.5<@BA*7
> +------------------------
>
> Notice the difference between the two bash results blocks. In the
> first, the input string is folded at column 60, without any other
> changes. In the second, a string of characters has been deleted:
>
> - `GGGFCF:,FF9>` from the beginning of the third line
> - `GC5>` from the beginning of the fourth line
>
> The fact that the deleted strings both start at the beginning of
> a line and end with a `>` suggests that the session thinks they should
> be redirected somehow, and in the process is dropping them completely.
> However, when I look at the session buffer, the output appears as
> expected, with no missing characters.
>
> How do I force the babel session to leave the output alone, and print
> it verbatim into the org file?
It may be related to other problems related to prompt in shell sessions.
See for example
<http://lists.gnu.org/r/emacs-orgmode/2018-02/msg00081.html>,
<http://lists.gnu.org/r/emacs-orgmode/2018-01/msg00415.html>, and for
step forward a solution
<http://lists.gnu.org/archive/html/emacs-orgmode/2017-04/msg00147.html>.
Patches welcome!
Regards,
--
Nicolas Goaziou
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: org alters output of bash code blocks when run with :session
2018-02-26 10:27 ` Nicolas Goaziou
@ 2018-03-13 17:24 ` Tyler Smith
2018-03-14 13:51 ` Nicolas Goaziou
0 siblings, 1 reply; 4+ messages in thread
From: Tyler Smith @ 2018-03-13 17:24 UTC (permalink / raw)
To: Nicolas Goaziou; +Cc: Emacs Org-Mode Help
On Mon, Feb 26, 2018, at 6:27 AM, Nicolas Goaziou wrote:
> Tyler Smith <tyler@plantarum.ca> writes:
> >
> > How do I force the babel session to leave the output alone, and print
> > it verbatim into the org file?
>
> It may be related to other problems related to prompt in shell sessions.
> See for example
> <http://lists.gnu.org/r/emacs-orgmode/2018-02/msg00081.html>,
> <http://lists.gnu.org/r/emacs-orgmode/2018-01/msg00415.html>, and for
> step forward a solution
> <http://lists.gnu.org/archive/html/emacs-orgmode/2017-04/msg00147.html>.
>
> Patches welcome!
It looks like ob-shell sets up sessions just by calling `shell`, which means all the user's customizations for shell-mode are automatically applied. This includes setting the prompt (e.g., from .emacs.d/init_bash.sh), as well as the value of `comint-prompt-regexp`.
I can't see any straightforward way to modify ob-shell sessions without also changing regular shell-mode. So I wonder if the easiest way to address this would be to create a new mode derived from shell-mode, ('ob-shell-mode')? That would give us a way to modify the prompt code inside babel without interfering with shell-mode.
If that sounds sensible I can put together a patch for ob-shell.el. Let me know what you think.
Best,
Tyler
^ permalink raw reply [flat|nested] 4+ messages in thread* Re: org alters output of bash code blocks when run with :session
2018-03-13 17:24 ` Tyler Smith
@ 2018-03-14 13:51 ` Nicolas Goaziou
0 siblings, 0 replies; 4+ messages in thread
From: Nicolas Goaziou @ 2018-03-14 13:51 UTC (permalink / raw)
To: Tyler Smith; +Cc: Emacs Org-Mode Help
Hello,
Tyler Smith <tyler@plantarum.ca> writes:
> I can't see any straightforward way to modify ob-shell sessions
> without also changing regular shell-mode. So I wonder if the easiest
> way to address this would be to create a new mode derived from
> shell-mode, ('ob-shell-mode')? That would give us a way to modify the
> prompt code inside babel without interfering with shell-mode.
Creating a new mode doesn't sound like the easiest way.
What about the following suggestion, from a link I posted in this
thread:
Thanks for the examples. Anything goes, of course, but I'm hoping for a
tighter integration. Maybe a :prompt param to sh source blocks, which
sets the prompt in a session, and which also manipulates
`comint-prompt-regexp' or `shell-prompt-pattern' local in the session buffer.
Or a mechanism like in Tramp, where the shell prompt is set to a random
string not expected in the shell (see `tramp-end-of-output'), and
`comint-prompt-regexp' or `shell-prompt-pattern' are adapted
automatically local in the session buffer.
Regards,
--
Nicolas Goaziou 0x80A93738
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2018-03-14 13:51 UTC | newest]
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2018-02-21 22:10 org alters output of bash code blocks when run with :session Tyler Smith
2018-02-26 10:27 ` Nicolas Goaziou
2018-03-13 17:24 ` Tyler Smith
2018-03-14 13:51 ` Nicolas Goaziou
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