* remote plot with local output?
@ 2015-09-14 15:11 Benda Xu
2015-09-14 16:48 ` Suvayu Ali
2015-09-14 20:42 ` Charles C. Berry
0 siblings, 2 replies; 10+ messages in thread
From: Benda Xu @ 2015-09-14 15:11 UTC (permalink / raw)
To: emacs-orgmode
Dear All,
I am looking for a way to configure org-babel so that a program runs
remotely and outputs locally. An example is
#+NAME: line
| 1 |
| 2 |
| 3 |
#+BEGIN_SRC python :results file :var dt=line :dir /ipmuap02:/tmp
from matplotlib import pylab as plt
plt.plot(dt)
plt.savefig("line.png")
return "line.png"
#+END_SRC
#+RESULTS:
[[file:/scp:ipmuap02:/tmp/line.png]]
I would like to embed this figure into my note. The example above need
to fetch the figure from the remote host on each exportation, which is
very sensitive to the network environment.
I cannot make the plot locally, because (unlike the over-simplified
example) some potentially big data are only available remotely.
My solution is to cache the result (:cache yes), execute the code block,
copy the output file to localhost, update the #+RESULTS link to the
local one, manually. Now I am facing many such tasks and feel like
automating that.
What is the recommended way for copying the file output from an remote
execution code block back to localhost?
BTW, my org-mode is 8.3.1 and emacs is 24.4.1.
Cheers,
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-14 15:11 remote plot with local output? Benda Xu
@ 2015-09-14 16:48 ` Suvayu Ali
2015-09-15 8:54 ` Benda Xu
2015-09-15 8:57 ` Benda Xu
2015-09-14 20:42 ` Charles C. Berry
1 sibling, 2 replies; 10+ messages in thread
From: Suvayu Ali @ 2015-09-14 16:48 UTC (permalink / raw)
To: emacs-orgmode
On Tue, Sep 15, 2015 at 12:11:03AM +0900, Benda Xu wrote:
>
> My solution is to cache the result (:cache yes), execute the code block,
> copy the output file to localhost, update the #+RESULTS link to the
> local one, manually. Now I am facing many such tasks and feel like
> automating that.
Maybe, you could do all that in your python source block? You could use
the :file header to specify where the plot gets copied to on the local
filesystem.
WDYT?
--
Suvayu
Open source is the future. It sets us free.
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-14 15:11 remote plot with local output? Benda Xu
2015-09-14 16:48 ` Suvayu Ali
@ 2015-09-14 20:42 ` Charles C. Berry
2015-09-15 8:28 ` Benda Xu
1 sibling, 1 reply; 10+ messages in thread
From: Charles C. Berry @ 2015-09-14 20:42 UTC (permalink / raw)
To: Benda Xu; +Cc: emacs-orgmode
On Tue, 15 Sep 2015, Benda Xu wrote:
> Dear All,
>
> I am looking for a way to configure org-babel so that a program runs
> remotely and outputs locally. An example is
>
> #+NAME: line
> | 1 |
> | 2 |
> | 3 |
>
> #+BEGIN_SRC python :results file :var dt=line :dir /ipmuap02:/tmp
> from matplotlib import pylab as plt
> plt.plot(dt)
> plt.savefig("line.png")
> return "line.png"
> #+END_SRC
>
> #+RESULTS:
> [[file:/scp:ipmuap02:/tmp/line.png]]
>
> I would like to embed this figure into my note. The example above need
> to fetch the figure from the remote host on each exportation, which is
> very sensitive to the network environment.
>
> I cannot make the plot locally, because (unlike the over-simplified
> example) some potentially big data are only available remotely.
>
> My solution is to cache the result (:cache yes), execute the code block,
> copy the output file to localhost, update the #+RESULTS link to the
> local one, manually. Now I am facing many such tasks and feel like
> automating that.
>
>
> What is the recommended way for copying the file output from an remote
> execution code block back to localhost?
>
Look at the :post header arg
(info "(org) post")
You write a src block that extracts the remote file name from *this*,
creates a local file name from it, copies the remote file to the local
host, then substitutes the local file name in *this* and uses it as the
return value.
Use the name of that src block as the argument to :post
HTH,
Chuck
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-14 20:42 ` Charles C. Berry
@ 2015-09-15 8:28 ` Benda Xu
2015-09-15 16:19 ` Charles C. Berry
0 siblings, 1 reply; 10+ messages in thread
From: Benda Xu @ 2015-09-15 8:28 UTC (permalink / raw)
To: emacs-orgmode
Hi Charles,
"Charles C. Berry" <ccberry@ucsd.edu> writes:
> Look at the :post header arg
>
> (info "(org) post")
>
> You write a src block that extracts the remote file name from *this*,
> creates a local file name from it, copies the remote file to the local
> host, then substitutes the local file name in *this* and uses it as
> the return value.
>
> Use the name of that src block as the argument to :post
Thanks for your hint. I come up with the following example:
#+NAME: line
| 1 |
| 2 |
| 3 |
#+name: localize
#+BEGIN_SRC emacs-lisp :var file="" dir=""
(let ((rfile (concat (file-name-as-directory dir) file)))
(let ((lfile (car (last (split-string rfile ":")))))
(copy-file rfile lfile 1)
lfile))
#+END_SRC
#+HEADER: :post localize(*this*, "/ipmuap02:/tmp")
#+BEGIN_SRC python :results file :var dt=line :dir /ipmuap02:/tmp
from matplotlib import pylab as plt
plt.plot(dt)
plt.savefig("line.png")
return "line.png"
#+END_SRC
#+RESULTS:
[[file:/tmp/line.png]]
*this* only returns the resulting file name, without :dir. I have to
set the same remote directory again in the :post call. Is there a
smarter way to achieve it without duplication?
Cheers,
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-14 16:48 ` Suvayu Ali
@ 2015-09-15 8:54 ` Benda Xu
2015-09-15 8:57 ` Benda Xu
1 sibling, 0 replies; 10+ messages in thread
From: Benda Xu @ 2015-09-15 8:54 UTC (permalink / raw)
To: emacs-orgmode
Hi Suvayu,
Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:
> Maybe, you could do all that in your python source block? You could use
> the :file header to specify where the plot gets copied to on the local
> filesystem.
>
> WDYT?
I did think of putting the logic into python source block. As I will
also have R block like this, having a language-neutral solution, like
:post, better suits.
BTW, how can one extract the string specified by :file inside a python
code block?
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-14 16:48 ` Suvayu Ali
2015-09-15 8:54 ` Benda Xu
@ 2015-09-15 8:57 ` Benda Xu
1 sibling, 0 replies; 10+ messages in thread
From: Benda Xu @ 2015-09-15 8:57 UTC (permalink / raw)
To: emacs-orgmode
Hi Suvayu,
Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:
> Maybe, you could do all that in your python source block? You could use
> the :file header to specify where the plot gets copied to on the local
> filesystem.
>
> WDYT?
I did think of putting the logic into python source block. As I will
also have R block like this, having a language-neutral solution, like
:post, better suits.
BTW, how can one extract the string specified by :file inside a python
code block?
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-15 8:28 ` Benda Xu
@ 2015-09-15 16:19 ` Charles C. Berry
2015-09-16 2:13 ` Benda Xu
0 siblings, 1 reply; 10+ messages in thread
From: Charles C. Berry @ 2015-09-15 16:19 UTC (permalink / raw)
To: Benda Xu; +Cc: emacs-orgmode
On Tue, 15 Sep 2015, Benda Xu wrote:
> Hi Charles,
>
> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>
>> Look at the :post header arg
>>
>> (info "(org) post")
>>
>> You write a src block that extracts the remote file name from *this*,
>> creates a local file name from it, copies the remote file to the local
>> host, then substitutes the local file name in *this* and uses it as
>> the return value.
>>
>> Use the name of that src block as the argument to :post
>
> Thanks for your hint. I come up with the following example:
>
> #+NAME: line
> | 1 |
> | 2 |
> | 3 |
>
> #+name: localize
> #+BEGIN_SRC emacs-lisp :var file="" dir=""
> (let ((rfile (concat (file-name-as-directory dir) file)))
> (let ((lfile (car (last (split-string rfile ":")))))
> (copy-file rfile lfile 1)
> lfile))
> #+END_SRC
>
> #+HEADER: :post localize(*this*, "/ipmuap02:/tmp")
> #+BEGIN_SRC python :results file :var dt=line :dir /ipmuap02:/tmp
> from matplotlib import pylab as plt
> plt.plot(dt)
> plt.savefig("line.png")
> return "line.png"
> #+END_SRC
>
> #+RESULTS:
> [[file:/tmp/line.png]]
>
> *this* only returns the resulting file name, without :dir. I have to
> set the same remote directory again in the :post call. Is there a
> smarter way to achieve it without duplication?
>
Untested, but try this :
#+name: localize
#+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
(let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
(rfile (concat (file-name-as-directory dir) file))
(lfile (car (last (split-string rfile ":")))))
(copy-file rfile lfile 1)
lfile)
#+END_SRC
then use
#+HEADER: :post localize(*this*)
in your python src block.
HTH,
Chuck
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-15 16:19 ` Charles C. Berry
@ 2015-09-16 2:13 ` Benda Xu
2015-09-18 8:58 ` Benda Xu
0 siblings, 1 reply; 10+ messages in thread
From: Benda Xu @ 2015-09-16 2:13 UTC (permalink / raw)
To: emacs-orgmode
Hi Charles,
"Charles C. Berry" <ccberry@ucsd.edu> writes:
> Untested, but try this :
>
> #+name: localize
> #+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
> (let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
> (rfile (concat (file-name-as-directory dir) file))
> (lfile (car (last (split-string rfile ":")))))
> (copy-file rfile lfile 1)
> lfile)
> #+END_SRC
>
> then use
>
> #+HEADER: :post localize(*this*)
>
> in your python src block.
It successfully extracts the :dir field. Thanks!
Cheers,
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-16 2:13 ` Benda Xu
@ 2015-09-18 8:58 ` Benda Xu
2015-09-18 18:11 ` Charles C. Berry
0 siblings, 1 reply; 10+ messages in thread
From: Benda Xu @ 2015-09-18 8:58 UTC (permalink / raw)
To: emacs-orgmode
Hi,
Benda Xu <heroxbd@gentoo.org> writes:
> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>
>> Untested, but try this :
>>
>> #+name: localize
>> #+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
>> (let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
>> (rfile (concat (file-name-as-directory dir) file))
>> (lfile (car (last (split-string rfile ":")))))
>> (copy-file rfile lfile 1)
>> lfile)
>> #+END_SRC
>>
>> then use
>>
>> #+HEADER: :post localize(*this*)
>>
>> in your python src block.
>
> It successfully extracts the :dir field. Thanks!
Python works this way. But babel R has a completely different *this*
value. Consider the following example:
#+BEGIN_SRC R :results output graphics :file line.png :dir /ipmuap02:/tmp
plot(c(1,2,3))
#+END_SRC
#+RESULTS:
[[file:/scp:ipmuap02:/tmp/line.png]]
*this* equals "[[file:/scp:ipmuap02:/tmp/line.png]]", but in babel
python *this* equals "line.png".
So I come up with
#+name: localize
#+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
(let ((lang (car srcinfo)))
(cond ((string= lang "python")
(let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
(rfile (concat (file-name-as-directory dir) file))
(lfile (car (last (split-string rfile ":")))))
(copy-file rfile lfile 1)
lfile))
((string= lang "R")
(let* ((rfile (substring file 7 -2))
(lfile (car (last (split-string rfile ":")))))
(copy-file rfile lfile 1)
(concat "[[file:" lfile "]]")))))
#+END_SRC
But the result is a string rather than a file link:
#+HEADER: :post localize(*this*)
#+BEGIN_SRC R :results output graphics :file line.png :dir /ipmuap02:/tmp
plot(c(1,2,3))
#+END_SRC
#+RESULTS:
: [[file:/tmp/line.png]]
Any hints?
Yours,
Benda
^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: remote plot with local output?
2015-09-18 8:58 ` Benda Xu
@ 2015-09-18 18:11 ` Charles C. Berry
0 siblings, 0 replies; 10+ messages in thread
From: Charles C. Berry @ 2015-09-18 18:11 UTC (permalink / raw)
To: Benda Xu; +Cc: emacs-orgmode
On Fri, 18 Sep 2015, Benda Xu wrote:
> Hi,
>
> Benda Xu <heroxbd@gentoo.org> writes:
>
>> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>>
>>> Untested, but try this :
>>>
>>> #+name: localize
>>> #+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
>>> (let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
>>> (rfile (concat (file-name-as-directory dir) file))
>>> (lfile (car (last (split-string rfile ":")))))
>>> (copy-file rfile lfile 1)
>>> lfile)
>>> #+END_SRC
>>>
>>> then use
>>>
>>> #+HEADER: :post localize(*this*)
>>>
>>> in your python src block.
>>
>> It successfully extracts the :dir field. Thanks!
>
> Python works this way. But babel R has a completely different *this*
> value. Consider the following example:
>
> #+BEGIN_SRC R :results output graphics :file line.png :dir /ipmuap02:/tmp
> plot(c(1,2,3))
> #+END_SRC
>
> #+RESULTS:
> [[file:/scp:ipmuap02:/tmp/line.png]]
>
> *this* equals "[[file:/scp:ipmuap02:/tmp/line.png]]", but in babel
> python *this* equals "line.png".
>
> So I come up with
>
> #+name: localize
> #+BEGIN_SRC emacs-lisp :var file="" srcinfo=(org-babel-get-src-block-info)
> (let ((lang (car srcinfo)))
> (cond ((string= lang "python")
> (let* ((dir (cdr (assoc :dir (nth 2 srcinfo))))
> (rfile (concat (file-name-as-directory dir) file))
> (lfile (car (last (split-string rfile ":")))))
> (copy-file rfile lfile 1)
> lfile))
> ((string= lang "R")
> (let* ((rfile (substring file 7 -2))
> (lfile (car (last (split-string rfile ":")))))
> (copy-file rfile lfile 1)
> (concat "[[file:" lfile "]]")))))
> #+END_SRC
>
> But the result is a string rather than a file link:
>
> #+HEADER: :post localize(*this*)
> #+BEGIN_SRC R :results output graphics :file line.png :dir /ipmuap02:/tmp
> plot(c(1,2,3))
> #+END_SRC
>
> #+RESULTS:
> : [[file:/tmp/line.png]]
>
> Any hints?
>
Forget *this* and use the
(cdr (assoc :file (nth 2 srcinfo))
to get the file name. That should work the same way regardless of
language.
Chuck
^ permalink raw reply [flat|nested] 10+ messages in thread
end of thread, other threads:[~2015-09-18 18:12 UTC | newest]
Thread overview: 10+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-09-14 15:11 remote plot with local output? Benda Xu
2015-09-14 16:48 ` Suvayu Ali
2015-09-15 8:54 ` Benda Xu
2015-09-15 8:57 ` Benda Xu
2015-09-14 20:42 ` Charles C. Berry
2015-09-15 8:28 ` Benda Xu
2015-09-15 16:19 ` Charles C. Berry
2015-09-16 2:13 ` Benda Xu
2015-09-18 8:58 ` Benda Xu
2015-09-18 18:11 ` Charles C. Berry
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