ob-shell: using a table variable with bash

ob-shell: using a table variable with bash

[George Kettleborough (EI)]

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Hello,

I recently updated my org-mode from version 7 (I think) to the latest. 
The behaviour of using a table as a variable in a shell code source 
block has changed. I use to use it like this:

#+BEGIN_SRC sh :results output :var table=synteny-names :separator ,
   IFS=','
   while read col1 col2; do
       # do stuff
   done <<EOF
   $table
   EOF
#+END_SRC

This just stopped working with the new version and I could not figure 
out why for a long time. But I looked in the new ob-shell.el code and 
figured out that when the shell is bash it now makes an associative 
array if the variable is a table. I couldn't seem to find this 
documented anywhere.

This new behaviour seems like it would be useful in a lot of cases, but 
in my case, the tables are not key-value pairs, they are merely things I 
want to iterate over. I wonder if simply checking to see if :separator 
is set and using the old behaviour if so would be better? This would 
seem to be a fine fix which maintains backwards compatibility unless 
there is a reason to set :separator but still expect the new behaviour.

Thanks,

George.

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diff --git a/site-lisp/org/ob-shell.el b/site-lisp/org/ob-shell.el
index 9c22af8..6f5f76e 100644
--- a/site-lisp/org/ob-shell.el
+++ b/site-lisp/org/ob-shell.el
@@ -140,7 +140,7 @@ This function is called by `org-babel-execute-src-block'."
 
 (defun org-babel--variable-assignments:bash (varname values &optional sep hline)
   "Represents the parameters as useful Bash shell variables."
-  (if (listp values)
+  (if (and (listp values) (null sep))
       (if (and (listp (car values)) (= 1 (length (car values))))
 	  (org-babel--variable-assignments:bash_array varname values sep hline)
 	(org-babel--variable-assignments:bash_assoc varname values sep hline))

Re: ob-shell: using a table variable with bash

[Nicolas Goaziou]

Hello,

"George Kettleborough (EI)" <george.kettleborough@earlham.ac.uk> writes:

> I recently updated my org-mode from version 7 (I think) to the latest. 
> The behaviour of using a table as a variable in a shell code source 
> block has changed. I use to use it like this:
>
> #+BEGIN_SRC sh :results output :var table=synteny-names :separator ,
>    IFS=','
>    while read col1 col2; do
>        # do stuff
>    done <<EOF
>    $table
>    EOF
> #+END_SRC
>
> This just stopped working with the new version and I could not figure 
> out why for a long time. But I looked in the new ob-shell.el code and 
> figured out that when the shell is bash it now makes an associative 
> array if the variable is a table. I couldn't seem to find this 
> documented anywhere.
>
> This new behaviour seems like it would be useful in a lot of cases, but 
> in my case, the tables are not key-value pairs, they are merely things I 
> want to iterate over. I wonder if simply checking to see if :separator 
> is set and using the old behaviour if so would be better? This would 
> seem to be a fine fix which maintains backwards compatibility unless 
> there is a reason to set :separator but still expect the new
> behaviour.

I have no objection to this patch, but I think it needs to be
documented, if only as a code comment. IIRC, there is also some
documentation about "ob-shell" on Worg. It would be nice to document
this feature.

Also, could you provide a proper commit message?

Thank you.

Regards,

-- 
Nicolas Goaziou

Re: ob-shell: using a table variable with bash

[George Kettleborough]

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On 08/03/17 08:24, Nicolas Goaziou wrote:
> I have no objection to this patch, but I think it needs to be
> documented, if only as a code comment. IIRC, there is also some
> documentation about "ob-shell" on Worg. It would be nice to document
> this feature.

I can't actually find any documentation for ob-shell. I had to read the 
source code. I have documented it as a code comment in my patch (with 
proper commit message).

Thanks,

George.


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From 97dadaf0ba0f18772d4d8ac968ea63374937b179 Mon Sep 17 00:00:00 2001
From: George Kettleborough <george.kettleborough@earlham.ac.uk>
Date: Wed, 8 Mar 2017 11:25:37 +0000
Subject: [PATCH] ob-shell: use old table var behaviour when sep is used

When using the bash shell and an org table is used as a variable, the
default behaviour is to declare it as a bash array. The generic
behaviour is to convert the table to a string with columns separated by
a given separator string. This allows a user to choose the generic
behaviour by declaring the separator using a :separator option to the
code block.
---
 lisp/ob-shell.el | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lisp/ob-shell.el b/lisp/ob-shell.el
index 9c22af8..8c7b4f1 100644
--- a/lisp/ob-shell.el
+++ b/lisp/ob-shell.el
@@ -140,7 +140,9 @@ This function is called by `org-babel-execute-src-block'."
 
 (defun org-babel--variable-assignments:bash (varname values &optional sep hline)
   "Represents the parameters as useful Bash shell variables."
-  (if (listp values)
+  ;; we declare org tables as bash array types, unless the user has
+  ;; set the :separator option
+  (if (and (listp values) (null sep))
       (if (and (listp (car values)) (= 1 (length (car values))))
 	  (org-babel--variable-assignments:bash_array varname values sep hline)
 	(org-babel--variable-assignments:bash_assoc varname values sep hline))
-- 
2.10.1.502.g6598894