Sharing variables between source blocks without session

Sharing variables between source blocks without session

[Loris Bennett]

Hi,

I have a 'sh' source block which produces a table which I then want to
plot with a 'python' source block:

#+NAME: code;raw_data
#+HEADER: :var user="loris"
#+BEGIN_SRC sh
  ps -u loris -o etimes=
#+END_SRC                                                                                                                                                                                                        

#+NAME: tab;raw_data
#+RESULTS: code;raw_data...

#+HEADER: :var df=tab;raw_data
#+HEADER: :var user="loris"
#+BEGIN_SRC python :results file :var f="process_times.pdf"
  import numpy as np
  import matplotlib.pyplot as plt
  # flatten list
  x = [item for sublist in df for item in sublist]
  plt.hist(x, bins=10)
  plt.xlabel("time [s]")
  plt.ylabel("number of processes")
  plt.title("user: " + user)
  plt.savefig(f) 
  return f
#+END_SRC

How can I avoid having to declare the variable 'user' for both blocks?

Cheers,

Loris

-- 
This signature is currently under construction.

Re: Sharing variables between source blocks without session

[Loris Bennett]

"Loris Bennett" <loris.bennett@fu-berlin.de> writes:

> Hi,
>
> I have a 'sh' source block which produces a table which I then want to
> plot with a 'python' source block:
>
> #+NAME: code;raw_data
> #+HEADER: :var user="loris"
>
> #+BEGIN_SRC sh
>   ps -u loris -o etimes=
> #+END_SRC

Oops, that should be 

#+NAME: code;raw_data
#+HEADER: :var user="loris"
#+BEGIN_SRC sh
  ps -u $user -o etimes=
#+END_SRC

> #+NAME: tab;raw_data
> #+RESULTS: code;raw_data...
>
> #+HEADER: :var df=tab;raw_data
> #+HEADER: :var user="loris"
>
> #+BEGIN_SRC python :results file :var f="process_times.pdf"
>   import numpy as np
>   import matplotlib.pyplot as plt
>   # flatten list
>   x = [item for sublist in df for item in sublist]
>   plt.hist(x, bins=10)
>   plt.xlabel("time [s]")
>   plt.ylabel("number of processes")
>   plt.title("user: " + user)
>   plt.savefig(f) 
>   return f
> #+END_SRC
>
> How can I avoid having to declare the variable 'user' for both blocks?
>
> Cheers,
>
> Loris
-- 
Dr. Loris Bennett (Hr./Mr.)
ZEDAT, Freie Universität Berlin         Email loris.bennett@fu-berlin.de

Re: Sharing variables between source blocks without session

[Eric S Fraga]

On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote:
> How can I avoid having to declare the variable 'user' for both blocks?

I imagine you could use a property, as in

#+property: header-args :var user=loris

or even make it specific for the particular language.

(untested)
-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.4-254-g37749c

Re: Sharing variables between source blocks without session

[Loris Bennett]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote:
>> How can I avoid having to declare the variable 'user' for both blocks?
>
> I imagine you could use a property, as in
>
> #+property: header-args :var user=loris
>
> or even make it specific for the particular language.
>
> (untested)

Thanks for point out using 'header-args;' as property.  However, if I do
the following, the variable is unset in the shell script:

#+properties: header-args :var user=loris

#+begin_src sh
  echo user: ${user}
#+end_src

#+RESULTS:
: user:

Is that supposed to work, or am I doing something wrong?

Cheers,

Loris

-- 
This signature is currently under construction.

Re: Sharing variables between source blocks without session

[Eric S Fraga]

On Thursday, 18 Mar 2021 at 14:21, Loris Bennett wrote:
> Thanks for point out using 'header-args;' as property.  However, if I do
> the following, the variable is unset in the shell script:

Works for me.

Make sure you reload properties by hitting C-c C-c on the property line
(or some other #+ meta line in the file).  Also, you will need to put
the value of the user variable in "quotes", i.e. user="loris", for some
reason.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.4-254-g37749c

Re: Sharing variables between source blocks without session

[Loris Bennett]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Thursday, 18 Mar 2021 at 14:21, Loris Bennett wrote:
>> Thanks for point out using 'header-args;' as property.  However, if I do
>> the following, the variable is unset in the shell script:
>
> Works for me.
>
> Make sure you reload properties by hitting C-c C-c on the property line
> (or some other #+ meta line in the file).  Also, you will need to put
> the value of the user variable in "quotes", i.e. user="loris", for some
> reason.

OK, works for me, too now.  The quotes were the important thing, thanks.

For future me and the future in general, would it be a good idea to add
an example to

  https://orgmode.org/manual/Using-Header-Arguments.html

which illustrates the difference between strings and numbers,
e.g.

#+property: header-args:sh :var user="loris" fails=3 temp=17.1

#+begin_src sh
  echo user ${user}
  echo fails ${fails}
  echo temp ${temp}
#+end_src

#+RESULTS:
| user  | loris |
| fails |     3 |
| temp  |  17.1 |

?

Cheers,

Loris

-- 
This signature is currently under construction.

RE: Sharing variables between source blocks without session

[Cook, Malcolm]

Eric S Fraga <mailto:e.fraga@ucl.ac.uk> writes:
>
>> On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote:
>>> How can I avoid having to declare the variable 'user' for both blocks?
>>
>> I imagine you could use a property, as in
>>
>> #+property: header-args :var user=loris
>>
>> or even make it specific for the particular language.
>>
>> (untested)
>
>Thanks for point out using 'header-args;' as property. However, if I do
>the following, the variable is unset in the shell script:
>
>#+properties: header-args :var user=loris
>
>#+begin_src sh
>echo user: ${user}
>#+end_src
>
>#+RESULTS:
>: user:
>
>Is that supposed to work, or am I doing something wrong?

I am unfamiliar with using the plural form of property, as you are trying, at buffer-level nor do I see  documented possible here:
https://orgmode.org/manual/Property-Syntax.html#Property-Syntax

try this:

#+property: header-args:sh :var user="loris"
#+begin_src sh
echo user: ${user}
#+end_src

Important: After adding or modifying the #+property line, you will need to instruct org to "refresh your local setup" which I typically accomplish by positioning the point on that line and typing C-c C-c

>
>Cheers,
>
>Loris
>
>-- 
>This signature is currently under construction.
>

Re: Sharing variables between source blocks without session

[Loris Bennett]

"Cook, Malcolm" <MEC@stowers.org> writes:

> Eric S Fraga <mailto:e.fraga@ucl.ac.uk> writes:
>>
>>> On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote:
>>>> How can I avoid having to declare the variable 'user' for both blocks?
>>>
>>> I imagine you could use a property, as in
>>>
>>> #+property: header-args :var user=loris
>>>
>>> or even make it specific for the particular language.
>>>
>>> (untested)
>>
>>Thanks for point out using 'header-args;' as property. However, if I do
>>the following, the variable is unset in the shell script:
>>
>>#+properties: header-args :var user=loris
>>
>>#+begin_src sh
>>echo user: ${user}
>>#+end_src
>>
>>#+RESULTS:
>>: user:
>>
>>Is that supposed to work, or am I doing something wrong?
>
> I am unfamiliar with using the plural form of property, as you are trying, at buffer-level nor do I see  documented possible here:
> https://orgmode.org/manual/Property-Syntax.html#Property-Syntax
>
> try this:
>
> #+property: header-args:sh :var user="loris"
> #+begin_src sh
>
> echo user: ${user}
> #+end_src
>
> Important: After adding or modifying the #+property line, you will need to instruct org to "refresh your local setup" which I typically accomplish by positioning the point on that line and typing C-c C-c

This doesn't work for me - there is no error, but I get the same result
as above, i.e. the variable ${users} is not set.  Does it work for you?  

What does work for me is using a section property rather than a buffer
property: 

* Dummy Section
  :PROPERTIES:
  :header-args: :R :var user="loris"
  :END:

#+begin_src sh
  echo user: ${user}
#+end_src

#+RESULTS:
: user: loris

However, the restriction to source blocks of a particular language does
not seem to work like this, but maybe I have got the syntax wrong
(again).

>
>>
>>Cheers,
>>
>>Loris
>>
>>-- 
>>This signature is currently under construction.
>>

Re: Sharing variables between source blocks without session

[Loris Bennett]

Loris Bennett <loris.bennett@fu-berlin.de> writes:

> "Cook, Malcolm" <MEC@stowers.org> writes:
>
>> Eric S Fraga <mailto:e.fraga@ucl.ac.uk> writes:
>>>
>>>> On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote:
>>>>> How can I avoid having to declare the variable 'user' for both blocks?
>>>>
>>>> I imagine you could use a property, as in
>>>>
>>>> #+property: header-args :var user=loris
>>>>
>>>> or even make it specific for the particular language.
>>>>
>>>> (untested)
>>>
>>>Thanks for point out using 'header-args;' as property. However, if I do
>>>the following, the variable is unset in the shell script:
>>>
>>>#+properties: header-args :var user=loris
>>>
>>>#+begin_src sh
>>>echo user: ${user}
>>>#+end_src
>>>
>>>#+RESULTS:
>>>: user:
>>>
>>>Is that supposed to work, or am I doing something wrong?
>>
>> I am unfamiliar with using the plural form of property, as you are trying, at
>> buffer-level nor do I see documented possible here:
>> https://orgmode.org/manual/Property-Syntax.html#Property-Syntax
>>
>> try this:
>>
>> #+property: header-args:sh :var user="loris"
>> #+begin_src sh
>>
>> echo user: ${user}
>> #+end_src
>>
>> Important: After adding or modifying the #+property line, you will need to
>> instruct org to "refresh your local setup" which I typically accomplish by
>> positioning the point on that line and typing C-c C-c
>
> This doesn't work for me - there is no error, but I get the same result
> as above, i.e. the variable ${users} is not set.  Does it work for you?  

Sorry, this does work for me.

> What does work for me is using a section property rather than a buffer
> property: 
>
> * Dummy Section
>   :PROPERTIES:
>   :header-args: :R :var user="loris"
>   :END:
>
> #+begin_src sh
>   echo user: ${user}
> #+end_src
>
> #+RESULTS:
> : user: loris
>
> However, the restriction to source blocks of a particular language does
> not seem to work like this, but maybe I have got the syntax wrong
> (again).

Quotes around string variables is the important thing.

>>
>>>
>>>Cheers,
>>>
>>>Loris
>>>
>>>-- 
>>>This signature is currently under construction.
>>>
>
>
-- 
This signature is currently under construction.

Re: Sharing variables between source blocks without session

[Eric S Fraga]

On Friday, 19 Mar 2021 at 07:38, Loris Bennett wrote:
> However, the restriction to source blocks of a particular language does
> not seem to work like this, but maybe I have got the syntax wrong
> (again).

Maybe ;-)

This seems to work for me for a shell:

:PROPERTIES:
:header-args:sh: :var user="loris"
:END:

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.4-254-g37749c

Re: Sharing variables between source blocks without session

[Loris Bennett]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Friday, 19 Mar 2021 at 07:38, Loris Bennett wrote:
>> However, the restriction to source blocks of a particular language does
>> not seem to work like this, but maybe I have got the syntax wrong
>> (again).
>
> Maybe ;-)
>
> This seems to work for me for a shell:
>
> :PROPERTIES:
> :header-args:sh: :var user="loris"
> :END:

That works for me, too.  The following correctly does not work:

  :PROPERTIES:
  :header-args:R: :var user="loris"
  :END:

  #+begin_src sh
    echo user ${user}
  #+end_src

  #+RESULTS:
  : user

To be honest, I find it is a wee bit confusing that it's

  #+PROPERTY: header-args:sh :var user="loris"

*without* a colon after the language (if I add it, there is not error,
but the variable is just not set) but

  :PROPERTIES:
  :header-args:sh: :var user="loris"
  :END:

*with* a colon after the language, but maybe I'm just easily confused
 :-)

Thanks for the help,

Loris
-- 
This signature is currently under construction.

Re: Sharing variables between source blocks without session

[Eric S Fraga]

On Friday, 19 Mar 2021 at 14:59, Loris Bennett wrote:
> To be honest, I find it is a wee bit confusing that it's
>
>   #+PROPERTY: header-args:sh :var user="loris"
>
> *without* a colon after the language (if I add it, there is not error,
> but the variable is just not set) but
>
>   :PROPERTIES:
>   :header-args:sh: :var user="loris"
>   :END:

When in a property drawer, the name of the property you want to set is
enclosed within a pair of :s.  When in a #+PROPERTY statement, there is
no need for the :s, just the name.  It's not about the language part of
it at all.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.4-254-g37749c

Re: Sharing variables between source blocks without session

[Loris Bennett]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Friday, 19 Mar 2021 at 14:59, Loris Bennett wrote:
>> To be honest, I find it is a wee bit confusing that it's
>>
>>   #+PROPERTY: header-args:sh :var user="loris"
>>
>> *without* a colon after the language (if I add it, there is not error,
>> but the variable is just not set) but
>>
>>   :PROPERTIES:
>>   :header-args:sh: :var user="loris"
>>   :END:
>
> When in a property drawer, the name of the property you want to set is
> enclosed within a pair of :s.  When in a #+PROPERTY statement, there is
> no need for the :s, just the name.  It's not about the language part of
> it at all.

Thanks for the clarification.  I didn't think it was about the language
part - I was just using the position describe which colon I meant.  The
colon gets to do quite a lot of work in Org :-)

Cheers,

Loris

-- 
This signature is currently under construction.