* org babel before excute hook
@ 2013-10-11 13:56 Henning Redestig
2013-10-11 20:31 ` John Kitchin
0 siblings, 1 reply; 11+ messages in thread
From: Henning Redestig @ 2013-10-11 13:56 UTC (permalink / raw)
To: emacs-orgmode
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I collaborate with different people on the same orgfile which contains many
source blocks that generate graphics by e.g. :results graphics abc.pdf
It can happen that I or someone else accidentally create another
independent source block that overwrites my abc.pdf which is of course very
bad.
I would like to add functionality so that org-babel-execute-src-block
checks if in :results graphics FILE, FILE is already referred to by another
source block and if so refuse to evaluate.
However, I only see a org-babel-after-execute-hook but no
org-babel-before-execute-hook
any reason for this? I could try to write a patch but thought I'd ask
first.
....or if there is an even better approach to avoid overwriting output from
different source blocks..
//Henning
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-11 13:56 org babel before excute hook Henning Redestig
@ 2013-10-11 20:31 ` John Kitchin
2013-10-12 2:28 ` Charles Berry
0 siblings, 1 reply; 11+ messages in thread
From: John Kitchin @ 2013-10-11 20:31 UTC (permalink / raw)
Cc: emacs-orgmode@gnu.org
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I have a related kind of problem. When preparing notes for a class, I may
end up with 70 code blocks in an org file, many of which create graphics. I
am always worried about accidentally using the same filename and
overwriting a graphic from an earlier block. A unique, but reproducible
filename would be sufficient for my needs.
John
John
-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu
On Fri, Oct 11, 2013 at 9:56 AM, Henning Redestig <henning.red@gmail.com>wrote:
> I collaborate with different people on the same orgfile which contains
> many source blocks that generate graphics by e.g. :results graphics abc.pdf
>
> It can happen that I or someone else accidentally create another
> independent source block that overwrites my abc.pdf which is of course very
> bad.
>
> I would like to add functionality so that org-babel-execute-src-block
> checks if in :results graphics FILE, FILE is already referred to by another
> source block and if so refuse to evaluate.
>
> However, I only see a org-babel-after-execute-hook but no
> org-babel-before-execute-hook
>
> any reason for this? I could try to write a patch but thought I'd ask
> first.
>
> ....or if there is an even better approach to avoid overwriting output
> from different source blocks..
>
> //Henning
>
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-11 20:31 ` John Kitchin
@ 2013-10-12 2:28 ` Charles Berry
2013-10-12 13:11 ` Henning Redestig
2013-10-13 21:22 ` Henning Redestig
0 siblings, 2 replies; 11+ messages in thread
From: Charles Berry @ 2013-10-12 2:28 UTC (permalink / raw)
To: emacs-orgmode
John Kitchin <jkitchin <at> andrew.cmu.edu> writes:
>
>
>
> I have a related kind of problem. When preparing notes
> for a class, I may end up with 70 code blocks in an org file, many of
> which create graphics. I am always worried about accidentally using the
> same filename and overwriting a graphic from an earlier block. A unique,
> but reproducible filename would be sufficient for my needs.
>
Header arg values can be elisp calls. You can use `make-temp-file'.
So every time this block is executed, a new file is created and the
file link is added to the results.
#+BEGIN_SRC R :results output append :file (make-temp-file "temp")
cat(date(),"\n")
#+END_SRC
#+RESULTS:
[[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp302IjV]]
[[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp3028Lu]]
See `temporary-file-directory', too, if you want to use this, as the
default may not be what you intend.
You might want to use this:
#+BEGIN_SRC emacs-lisp
(defun local-tfile (file)
(let ((temporary-file-directory "."))
(make-temp-file file)))
#+END_SRC
Then the files go in the local directory when this is executed:
#+BEGIN_SRC R :file (local-tfile "tfile") :results output append
cat(date(),"\n")
#+END_SRC
You might not want `append' in this case.
HTH,
Chuck
[rest deleted]
^ permalink raw reply [flat|nested] 11+ messages in thread* Re: org babel before excute hook
2013-10-12 2:28 ` Charles Berry
@ 2013-10-12 13:11 ` Henning Redestig
2013-10-13 21:22 ` Henning Redestig
1 sibling, 0 replies; 11+ messages in thread
From: Henning Redestig @ 2013-10-12 13:11 UTC (permalink / raw)
Cc: emacs-orgmode
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I thought about temp files, but that makes the file names cryptic which is
inconvenient for communication without people outside org.. also, I tend
recompile figures many times which would cause a lot of cluttering files
that are hard to delete since you don't know which file is the one
currently linked in your org file...
Anyway, I made this instead which appears to work as I intended
(defun org-babel-about-to-overwrite-file ()
(let ((info (org-babel-get-src-block-info)))
(setq result-file (cdr (assoc :file (nth 2 info))))
(if (save-excursion
(goto-char 0)
(re-search-forward (concat ":file +" result-file) nil t)
(re-search-forward (concat ":file +" result-file) nil t))
(message (concat result-file " defined in more than one source block"))
(org-babel-execute-maybe))))
(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-about-to-overwrite-file)
2013/10/12 Charles Berry <ccberry@ucsd.edu>
> John Kitchin <jkitchin <at> andrew.cmu.edu> writes:
>
> >
> >
> >
> > I have a related kind of problem. When preparing notes
> > for a class, I may end up with 70 code blocks in an org file, many of
> > which create graphics. I am always worried about accidentally using the
> > same filename and overwriting a graphic from an earlier block. A unique,
> > but reproducible filename would be sufficient for my needs.
> >
>
> Header arg values can be elisp calls. You can use `make-temp-file'.
>
> So every time this block is executed, a new file is created and the
> file link is added to the results.
>
> #+BEGIN_SRC R :results output append :file (make-temp-file "temp")
> cat(date(),"\n")
> #+END_SRC
>
> #+RESULTS:
> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp302IjV]]
> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp3028Lu]]
>
> See `temporary-file-directory', too, if you want to use this, as the
> default may not be what you intend.
>
>
> You might want to use this:
>
> #+BEGIN_SRC emacs-lisp
> (defun local-tfile (file)
> (let ((temporary-file-directory "."))
> (make-temp-file file)))
> #+END_SRC
>
> Then the files go in the local directory when this is executed:
>
> #+BEGIN_SRC R :file (local-tfile "tfile") :results output append
> cat(date(),"\n")
> #+END_SRC
>
> You might not want `append' in this case.
>
>
> HTH,
>
> Chuck
>
> [rest deleted]
>
>
>
>
>
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^ permalink raw reply [flat|nested] 11+ messages in thread* Re: org babel before excute hook
2013-10-12 2:28 ` Charles Berry
2013-10-12 13:11 ` Henning Redestig
@ 2013-10-13 21:22 ` Henning Redestig
2013-10-13 21:35 ` Samuel Wales
2013-10-14 13:29 ` Eric Schulte
1 sibling, 2 replies; 11+ messages in thread
From: Henning Redestig @ 2013-10-13 21:22 UTC (permalink / raw)
To: emacs-orgmode
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Is it possible to add a function to org-ctrl-c-ctrl-c-hook without patching
ob-core.el? If I just add something like
(add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-stop-if-file-collision)
in my .emacs I notice that my addition gets overwritten later via the
autoloads (I think) that are defined in ob-core.el..
2013/10/12 Charles Berry <ccberry@ucsd.edu>
> John Kitchin <jkitchin <at> andrew.cmu.edu> writes:
>
> >
> >
> >
> > I have a related kind of problem. When preparing notes
> > for a class, I may end up with 70 code blocks in an org file, many of
> > which create graphics. I am always worried about accidentally using the
> > same filename and overwriting a graphic from an earlier block. A unique,
> > but reproducible filename would be sufficient for my needs.
> >
>
> Header arg values can be elisp calls. You can use `make-temp-file'.
>
> So every time this block is executed, a new file is created and the
> file link is added to the results.
>
> #+BEGIN_SRC R :results output append :file (make-temp-file "temp")
> cat(date(),"\n")
> #+END_SRC
>
> #+RESULTS:
> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp302IjV]]
> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp3028Lu]]
>
> See `temporary-file-directory', too, if you want to use this, as the
> default may not be what you intend.
>
>
> You might want to use this:
>
> #+BEGIN_SRC emacs-lisp
> (defun local-tfile (file)
> (let ((temporary-file-directory "."))
> (make-temp-file file)))
> #+END_SRC
>
> Then the files go in the local directory when this is executed:
>
> #+BEGIN_SRC R :file (local-tfile "tfile") :results output append
> cat(date(),"\n")
> #+END_SRC
>
> You might not want `append' in this case.
>
>
> HTH,
>
> Chuck
>
> [rest deleted]
>
>
>
>
>
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^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-13 21:22 ` Henning Redestig
@ 2013-10-13 21:35 ` Samuel Wales
2013-10-14 6:45 ` Henning Redestig
2013-10-14 13:24 ` Eric Schulte
2013-10-14 13:29 ` Eric Schulte
1 sibling, 2 replies; 11+ messages in thread
From: Samuel Wales @ 2013-10-13 21:35 UTC (permalink / raw)
To: Henning Redestig; +Cc: emacs-orgmode
In case it helps, there is org-confirm-babel-evaluate.
(But I have not found it to be useful, because it does not seem to
place point in a place where you can check properties, etc.)
Samuel
--
The Kafka Pandemic: http://thekafkapandemic.blogspot.com
The disease DOES progress. MANY people have died from it. ANYBODY can get it.
Denmark: free Karina Hansen NOW.
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-13 21:35 ` Samuel Wales
@ 2013-10-14 6:45 ` Henning Redestig
2013-10-14 8:11 ` [babel] Feature request - WAS: " Rainer M Krug
2013-10-14 13:24 ` Eric Schulte
1 sibling, 1 reply; 11+ messages in thread
From: Henning Redestig @ 2013-10-14 6:45 UTC (permalink / raw)
To: emacs-orgmode; +Cc: John Kitchin
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if anyone is interested in this, a simple defadvice appears to be a good
option, I put
(defadvice org-babel-execute-maybe (around org-babel-stop-on-collision)
"stop execution of result file defined more than once"
(let ((info (org-babel-get-src-block-info)))
(setq result-file (cdr (assoc :file (nth 2 info))))
(if (save-excursion
(goto-char 0)
(re-search-forward (concat ":file +" result-file) nil t)
(re-search-forward (concat ":file +" result-file) nil t))
(error (concat result-file " defined in more than one source
block"))
ad-do-it)))
(ad-activate 'org-babel-execute-maybe)
in my .emacs and appear to get the desired functionality
2013/10/13 Samuel Wales <samologist@gmail.com>
> In case it helps, there is org-confirm-babel-evaluate.
>
> (But I have not found it to be useful, because it does not seem to
> place point in a place where you can check properties, etc.)
>
> Samuel
>
> --
> The Kafka Pandemic: http://thekafkapandemic.blogspot.com
>
> The disease DOES progress. MANY people have died from it. ANYBODY can
> get it.
>
> Denmark: free Karina Hansen NOW.
>
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^ permalink raw reply [flat|nested] 11+ messages in thread* [babel] Feature request - WAS: org babel before excute hook
2013-10-14 6:45 ` Henning Redestig
@ 2013-10-14 8:11 ` Rainer M Krug
0 siblings, 0 replies; 11+ messages in thread
From: Rainer M Krug @ 2013-10-14 8:11 UTC (permalink / raw)
To: emacs-orgmode
At the moment, I have the feeling that there is no solution to the
actual problem (avoiding duplicate :file names) without doctoring in an
unsatisfying (and potentially fragile?) way.
I would therefore formulate a feature request:
It is a common error to accidentally use the same :file name and to have
consequently the wrong file in the exported file.
I would therefore suggest a property with the following possible values:
,----
| file_unique
|
| - false :: the actual behaviour, i.e. consequtive :file overwrite the
| original ones *without* warning
| - true :: if more then one :file exist, an consecutive number is automatically
| to the :file and cached to avoid having leftover files (as in temp files)
| - warn :: give a warning on export, so that this error can be fixed
| manually.
`----
I would see this as a valuable addition to the export feature as it
avoids errors.
Cheers,
Rainer
Henning Redestig <henning.red@gmail.com> writes:
> if anyone is interested in this, a simple defadvice appears to be a good
> option, I put
>
> (defadvice org-babel-execute-maybe (around org-babel-stop-on-collision)
> "stop execution of result file defined more than once"
> (let ((info (org-babel-get-src-block-info)))
> (setq result-file (cdr (assoc :file (nth 2 info))))
> (if (save-excursion
> (goto-char 0)
> (re-search-forward (concat ":file +" result-file) nil t)
> (re-search-forward (concat ":file +" result-file) nil t))
> (error (concat result-file " defined in more than one source
> block"))
> ad-do-it)))
> (ad-activate 'org-babel-execute-maybe)
>
>
> in my .emacs and appear to get the desired functionality
>
>
>
>
> 2013/10/13 Samuel Wales <samologist@gmail.com>
>
>> In case it helps, there is org-confirm-babel-evaluate.
>>
>> (But I have not found it to be useful, because it does not seem to
>> place point in a place where you can check properties, etc.)
>>
>> Samuel
>>
>> --
>> The Kafka Pandemic: http://thekafkapandemic.blogspot.com
>>
>> The disease DOES progress. MANY people have died from it. ANYBODY can
>> get it.
>>
>> Denmark: free Karina Hansen NOW.
>>
<#secure method=pgpmime mode=sign>
--
Rainer M. Krug
email: RMKrug<at>gmail<dot>com
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-13 21:35 ` Samuel Wales
2013-10-14 6:45 ` Henning Redestig
@ 2013-10-14 13:24 ` Eric Schulte
2013-10-26 22:05 ` Samuel Wales
1 sibling, 1 reply; 11+ messages in thread
From: Eric Schulte @ 2013-10-14 13:24 UTC (permalink / raw)
To: Samuel Wales; +Cc: emacs-orgmode, Henning Redestig
Samuel Wales <samologist@gmail.com> writes:
> In case it helps, there is org-confirm-babel-evaluate.
>
> (But I have not found it to be useful, because it does not seem to
> place point in a place where you can check properties, etc.)
>
I just pushed up a change so that `org-confirm-babel-evaluate' will
always be called from the head of the code block being evaluated. So
the info can always be reached with something like the following.
(setf org-confirm-babel-evaluate
(lambda (&rest args)
(message "info: %S" (org-babel-get-src-block-info 'light))
nil))
>
> Samuel
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
^ permalink raw reply [flat|nested] 11+ messages in thread* Re: org babel before excute hook
2013-10-14 13:24 ` Eric Schulte
@ 2013-10-26 22:05 ` Samuel Wales
0 siblings, 0 replies; 11+ messages in thread
From: Samuel Wales @ 2013-10-26 22:05 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode, Henning Redestig
I have confirmed that this works. Thank you.
On 10/14/13, Eric Schulte <schulte.eric@gmail.com> wrote:
> I just pushed up a change so that `org-confirm-babel-evaluate' will
> always be called from the head of the code block being evaluated. So
> the info can always be reached with something like the following.
>
> (setf org-confirm-babel-evaluate
> (lambda (&rest args)
> (message "info: %S" (org-babel-get-src-block-info 'light))
> nil))
--
The Kafka Pandemic: http://thekafkapandemic.blogspot.com
The disease DOES progress. MANY people have died from it. ANYBODY can get it.
Denmark: free Karina Hansen NOW.
^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: org babel before excute hook
2013-10-13 21:22 ` Henning Redestig
2013-10-13 21:35 ` Samuel Wales
@ 2013-10-14 13:29 ` Eric Schulte
1 sibling, 0 replies; 11+ messages in thread
From: Eric Schulte @ 2013-10-14 13:29 UTC (permalink / raw)
To: Henning Redestig; +Cc: emacs-orgmode
Henning Redestig <henning.red@gmail.com> writes:
> Is it possible to add a function to org-ctrl-c-ctrl-c-hook without patching
> ob-core.el? If I just add something like
>
Yes, see the documentation of `org-confirm-babel-evaluate'. So the
function posted in your previous email could be changed to something
like...
(setf org-confirm-babel-evaluate
(lambda (&rest args)
(let* ((info (org-babel-get-src-block-info))
(result-file (cdr (assoc :file (nth 2 info))))
(duplicat-file-p
(save-excursion
(goto-char 0)
(re-search-forward (concat ":file +" result-file) nil t)
(re-search-forward (concat ":file +" result-file) nil t)))))
(if duplicate-file-p
(prog1 t (message "duplicate result file"))
nil)))
>
> (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-stop-if-file-collision)
>
> in my .emacs I notice that my addition gets overwritten later via the
> autoloads (I think) that are defined in ob-core.el..
>
>
>
> 2013/10/12 Charles Berry <ccberry@ucsd.edu>
>
>> John Kitchin <jkitchin <at> andrew.cmu.edu> writes:
>>
>> >
>> >
>> >
>> > I have a related kind of problem. When preparing notes
>> > for a class, I may end up with 70 code blocks in an org file, many of
>> > which create graphics. I am always worried about accidentally using the
>> > same filename and overwriting a graphic from an earlier block. A unique,
>> > but reproducible filename would be sufficient for my needs.
>> >
>>
>> Header arg values can be elisp calls. You can use `make-temp-file'.
>>
>> So every time this block is executed, a new file is created and the
>> file link is added to the results.
>>
>> #+BEGIN_SRC R :results output append :file (make-temp-file "temp")
>> cat(date(),"\n")
>> #+END_SRC
>>
>> #+RESULTS:
>> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp302IjV]]
>> [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/temp3028Lu]]
>>
>> See `temporary-file-directory', too, if you want to use this, as the
>> default may not be what you intend.
>>
>>
>> You might want to use this:
>>
>> #+BEGIN_SRC emacs-lisp
>> (defun local-tfile (file)
>> (let ((temporary-file-directory "."))
>> (make-temp-file file)))
>> #+END_SRC
>>
>> Then the files go in the local directory when this is executed:
>>
>> #+BEGIN_SRC R :file (local-tfile "tfile") :results output append
>> cat(date(),"\n")
>> #+END_SRC
>>
>> You might not want `append' in this case.
>>
>>
>> HTH,
>>
>> Chuck
>>
>> [rest deleted]
>>
>>
>>
>>
>>
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
^ permalink raw reply [flat|nested] 11+ messages in thread
end of thread, other threads:[~2013-10-26 22:05 UTC | newest]
Thread overview: 11+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2013-10-11 13:56 org babel before excute hook Henning Redestig
2013-10-11 20:31 ` John Kitchin
2013-10-12 2:28 ` Charles Berry
2013-10-12 13:11 ` Henning Redestig
2013-10-13 21:22 ` Henning Redestig
2013-10-13 21:35 ` Samuel Wales
2013-10-14 6:45 ` Henning Redestig
2013-10-14 8:11 ` [babel] Feature request - WAS: " Rainer M Krug
2013-10-14 13:24 ` Eric Schulte
2013-10-26 22:05 ` Samuel Wales
2013-10-14 13:29 ` Eric Schulte
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