* [babel] noweb reference with default values
@ 2015-12-14 13:28 Andreas Leha
2015-12-14 16:45 ` Charles C. Berry
0 siblings, 1 reply; 4+ messages in thread
From: Andreas Leha @ 2015-12-14 13:28 UTC (permalink / raw)
To: emacs-orgmode
Hi all,
I'd like to hear your ideas on how to include noweb references to code
blocks in a way that the default values are used as parameter values.
Here is a little example:
#+PROPERTY: header-args:R :session *testR*
The background is that I like to use Org mode table to record small data.
#+name: datatable
| A | B |
|---+----|
| 1 | 10 |
| 2 | 20 |
Usually I want to pre-process and/or convert such data.
#+name: read_datatable
#+header: :var datatable=datatable
#+begin_src R :results none
datatable$B <- 10 * datatable$B
#+end_src
Later I would like to use that data in larger (R-) code blocks. I'd
like such code blocks to DWIM:
#+name: some_code
#+begin_src R :noweb yes :results graphics :file testplot.png
<<read_datatable>>
plot(datatable$A, datatable$B)
#+end_src
But they do not: They are not stand alone and do not execute -- unless I
executed `read_datatable' manually/by chance upfront.
My current solution is to export the table to csv and read that csv in
`read_datatable'.
If the result of `read_datatable' is a single table again (as in this
MWE) I usually return that to Org mode which works ok. But often the
result is more complex than that.
I see two ways to go:
- I could serialize more complex objects to disk and return a file name.
But I'd prefer to not go through disk.
- I could pass the same arguments as to `read_datatable' also to
`some_code'. But that is duplication and becomes quite convoluted in
the case of several noweb references with several arguments each.
Any ideas how to do that better?
Thanks,
Andreas
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [babel] noweb reference with default values
2015-12-14 13:28 [babel] noweb reference with default values Andreas Leha
@ 2015-12-14 16:45 ` Charles C. Berry
2015-12-14 22:18 ` Andreas Leha
0 siblings, 1 reply; 4+ messages in thread
From: Charles C. Berry @ 2015-12-14 16:45 UTC (permalink / raw)
To: Andreas Leha; +Cc: emacs-orgmode
On Mon, 14 Dec 2015, Andreas Leha wrote:
> Hi all,
>
> I'd like to hear your ideas on how to include noweb references to code
> blocks in a way that the default values are used as parameter values.
>
> Here is a little example:
>
> #+PROPERTY: header-args:R :session *testR*
>
> The background is that I like to use Org mode table to record small data.
>
> #+name: datatable
> | A | B |
> |---+----|
> | 1 | 10 |
> | 2 | 20 |
>
> Usually I want to pre-process and/or convert such data.
>
> #+name: read_datatable
> #+header: :var datatable=datatable
> #+begin_src R :results none
> datatable$B <- 10 * datatable$B
> #+end_src
>
> Later I would like to use that data in larger (R-) code blocks. I'd
> like such code blocks to DWIM:
>
> #+name: some_code
> #+begin_src R :noweb yes :results graphics :file testplot.png
> <<read_datatable>>
> plot(datatable$A, datatable$B)
> #+end_src
>
> But they do not: They are not stand alone and do not execute -- unless I
> executed `read_datatable' manually/by chance upfront.
Try this:
#+name: read_datatable
#+header: :var datatable=datatable
#+begin_src R :results value :colnames yes
datatable$B <- 10 * datatable$B
datatable
#+end_src
#+name: some_code
#+HEADER: :var datatable=read_datatable()
#+begin_src R :noweb yes :results graphics :file testplot.png
plot(datatable$A, datatable$B)
#+end_src
HTH,
Chuck
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [babel] noweb reference with default values
2015-12-14 16:45 ` Charles C. Berry
@ 2015-12-14 22:18 ` Andreas Leha
2015-12-17 11:47 ` Andreas Leha
0 siblings, 1 reply; 4+ messages in thread
From: Andreas Leha @ 2015-12-14 22:18 UTC (permalink / raw)
To: emacs-orgmode
Hi Chuck,
"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Mon, 14 Dec 2015, Andreas Leha wrote:
>
>> Hi all,
>>
>> I'd like to hear your ideas on how to include noweb references to code
>> blocks in a way that the default values are used as parameter values.
>>
>> Here is a little example:
>>
>> #+PROPERTY: header-args:R :session *testR*
>>
>> The background is that I like to use Org mode table to record small data.
>>
>> #+name: datatable
>> | A | B |
>> |---+----|
>> | 1 | 10 |
>> | 2 | 20 |
>>
>> Usually I want to pre-process and/or convert such data.
>>
>> #+name: read_datatable
>> #+header: :var datatable=datatable
>> #+begin_src R :results none
>> datatable$B <- 10 * datatable$B
>> #+end_src
>>
>> Later I would like to use that data in larger (R-) code blocks. I'd
>> like such code blocks to DWIM:
>>
>> #+name: some_code
>> #+begin_src R :noweb yes :results graphics :file testplot.png
>> <<read_datatable>>
>> plot(datatable$A, datatable$B)
>> #+end_src
>>
>> But they do not: They are not stand alone and do not execute -- unless I
>> executed `read_datatable' manually/by chance upfront.
>
> Try this:
>
> #+name: read_datatable
> #+header: :var datatable=datatable
>
> #+begin_src R :results value :colnames yes
> datatable$B <- 10 * datatable$B
> datatable
> #+end_src
>
> #+name: some_code
> #+HEADER: :var datatable=read_datatable()
>
> #+begin_src R :noweb yes :results graphics :file testplot.png
> plot(datatable$A, datatable$B)
> #+end_src
>
Thanks! I am aware of that possibility. Should have posted a more
involved example. This works if I only return a table. Or something
else, that can be passed through Org. But it fails for instance if the
result is a function (or more functions...).
Regards,
Andreas
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [babel] noweb reference with default values
2015-12-14 22:18 ` Andreas Leha
@ 2015-12-17 11:47 ` Andreas Leha
0 siblings, 0 replies; 4+ messages in thread
From: Andreas Leha @ 2015-12-17 11:47 UTC (permalink / raw)
To: emacs-orgmode
Hi all,
Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
> Hi Chuck,
>
> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>> On Mon, 14 Dec 2015, Andreas Leha wrote:
>>
>>> Hi all,
>>>
>>> I'd like to hear your ideas on how to include noweb references to code
>>> blocks in a way that the default values are used as parameter values.
>>>
>>> Here is a little example:
>>>
>>> #+PROPERTY: header-args:R :session *testR*
>>>
>>> The background is that I like to use Org mode table to record small data.
>>>
>>> #+name: datatable
>>> | A | B |
>>> |---+----|
>>> | 1 | 10 |
>>> | 2 | 20 |
>>>
>>> Usually I want to pre-process and/or convert such data.
>>>
>>> #+name: read_datatable
>>> #+header: :var datatable=datatable
>>> #+begin_src R :results none
>>> datatable$B <- 10 * datatable$B
>>> #+end_src
>>>
>>> Later I would like to use that data in larger (R-) code blocks. I'd
>>> like such code blocks to DWIM:
>>>
>>> #+name: some_code
>>> #+begin_src R :noweb yes :results graphics :file testplot.png
>>> <<read_datatable>>
>>> plot(datatable$A, datatable$B)
>>> #+end_src
>>>
>>> But they do not: They are not stand alone and do not execute -- unless I
>>> executed `read_datatable' manually/by chance upfront.
>>
>> Try this:
>>
>> #+name: read_datatable
>> #+header: :var datatable=datatable
>>
>> #+begin_src R :results value :colnames yes
>> datatable$B <- 10 * datatable$B
>> datatable
>> #+end_src
>>
>> #+name: some_code
>> #+HEADER: :var datatable=read_datatable()
>>
>> #+begin_src R :noweb yes :results graphics :file testplot.png
>> plot(datatable$A, datatable$B)
>> #+end_src
>>
>
> Thanks! I am aware of that possibility. Should have posted a more
> involved example. This works if I only return a table. Or something
> else, that can be passed through Org. But it fails for instance if the
> result is a function (or more functions...).
>
In case anyone is interested. I came up with a quite simple code block
that does what I want:
--8<---------------cut here---------------start------------->8---
#+name: org_exec
#+header: :var srcblock=""
#+begin_src emacs-lisp :results silent
(save-excursion
(org-babel-goto-named-src-block srcblock)
(org-babel-execute-src-block)
)
(concat srcblock " executed")
#+end_src
--8<---------------cut here---------------end--------------->8---
Now, I can do
--8<---------------cut here---------------start------------->8---
#+name: some_code
#+begin_src R :session *testR* :noweb yes :results graphics :file testplot.png
<<org_exec("read_datatable")>>
plot(datatable$A, datatable$B)
#+end_src
--8<---------------cut here---------------end--------------->8---
The remaining downside is that I have to take care of running things in
the correct session.
Best,
Andreas
PS: complete example:
--8<---------------cut here---------------start------------->8---
* Org
#+name: org_exec
#+header: :var srcblock=""
#+begin_src emacs-lisp :results silent
(save-excursion
(org-babel-goto-named-src-block srcblock)
(org-babel-execute-src-block)
)
(concat "\"" srcblock " executed" "\"")
#+end_src
* Data
#+name: datatable
| A | B |
|---+----|
| 1 | 10 |
| 2 | 20 |
#+name: read_datatable
#+header: :var datatable=datatable
#+begin_src R :session *testR* :results value :colnames yes
datatable$B <- 10 * datatable$B
datatable
#+end_src
#+results: read_datatable
| A | B |
|---+-----|
| 1 | 100 |
| 2 | 200 |
* Analysis
#+name: some_code
#+begin_src R :session *testR* :noweb yes :results graphics :file testplot.png
<<org_exec("read_datatable")>>
plot(datatable$A, datatable$B)
#+end_src
#+results: some_code
[[file:testplot.png]]
--8<---------------cut here---------------end--------------->8---
^ permalink raw reply [flat|nested] 4+ messages in thread
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2015-12-14 13:28 [babel] noweb reference with default values Andreas Leha
2015-12-14 16:45 ` Charles C. Berry
2015-12-14 22:18 ` Andreas Leha
2015-12-17 11:47 ` Andreas Leha
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