* ob-shell: using a table variable with bash
@ 2017-03-03 12:40 George Kettleborough (EI)
2017-03-08 8:24 ` Nicolas Goaziou
0 siblings, 1 reply; 3+ messages in thread
From: George Kettleborough (EI) @ 2017-03-03 12:40 UTC (permalink / raw)
To: emacs-orgmode
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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.
[-- Attachment #2: ob-shell.patch --]
[-- Type: text/x-patch, Size: 661 bytes --]
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))
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: ob-shell: using a table variable with bash
2017-03-03 12:40 ob-shell: using a table variable with bash George Kettleborough (EI)
@ 2017-03-08 8:24 ` Nicolas Goaziou
2017-03-08 11:27 ` George Kettleborough
0 siblings, 1 reply; 3+ messages in thread
From: Nicolas Goaziou @ 2017-03-08 8:24 UTC (permalink / raw)
To: George Kettleborough (EI); +Cc: emacs-orgmode
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
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: ob-shell: using a table variable with bash
2017-03-08 8:24 ` Nicolas Goaziou
@ 2017-03-08 11:27 ` George Kettleborough
0 siblings, 0 replies; 3+ messages in thread
From: George Kettleborough @ 2017-03-08 11:27 UTC (permalink / raw)
To: Nicolas Goaziou; +Cc: emacs-orgmode
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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.
[-- Attachment #2: 0001-ob-shell-use-old-table-var-behaviour-when-sep-is-use.patch --]
[-- Type: text/x-patch, Size: 1431 bytes --]
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
^ permalink raw reply related [flat|nested] 3+ messages in thread
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