Passing a table to org-babel shell script

Passing a table to org-babel shell script

[Matthias Teege]

Hello,

I try to use a org-mode table as input to an shell script. It works, if
I use a Table with one column.

#+tblname: sec
| Hello World |

#+begin_src sh :var table=sec
cat <<EOF
$table
EOF
#+end_src

#+results:
: [[Hello World]]

But if I use more then one column, If got an error:

#+tblname: sec
| Hello | World |

#+begin_src sh :var table=sec
cat <<EOF
$table
EOF
#+end_src

#+results:
| sh: Zeile 1: World]]: command not found. |

It looks like, then Shell interprets the seperator "|" as pipe.

How do I use a multicolumn table as input for a shell script?

Many thanks
Matthias

Re: Passing a table to org-babel shell script

[Eric Schulte]

Hi Matthias,

Sorry about the slow reply.  This is a good question, I have comments
in-line below.

Matthias Teege <matthias-omd@mteege.de> writes:

[...]

> But if I use more then one column, If got an error:
>
> #+tblname: sec
> | Hello | World |
>
> #+begin_src sh :var table=sec
> cat <<EOF
> $table
> EOF
> #+end_src
>
> #+results:
> | sh: Zeile 1: World]]: command not found. |
>
> It looks like, then Shell interprets the seperator "|" as pipe.
>
> How do I use a multicolumn table as input for a shell script?
>

This is a good question, clearly the current approach of dumping it in
as a string isn't working, however I'm not sure what a good alternative
would be.  Some ideas that come to mind are...

1) allowing the user to specify a separator with a header argument as
   follows
   #+begin_src sh :var table=sec :separator ,
     cat <<EOF
     $table
     EOF
   #+end_src
   
   which would result in something like

   : "Hello, World"

2) writing the table to a tab or comma separated file and then
   replacing =$table= in the source block body with the path to the
   file name, s.t. something like
   
   #+begin_src sh :var table=data
     wc $table
   #+end_src

   would return reasonable results

I guess this would largely depend on what types of values you are
passing to the shell, and what your use-case is.

I'd be interested to hear other people's feedback here as the "right"
solution will be largely dependent on how people would actually be using
tables in shell scripts.

Thanks for bringing this up! -- Eric

Re: Passing a table to org-babel shell script

[Matthias Teege]

On 11:33 Sat 06 Feb, Eric Schulte wrote:

Moin,

thanks for your reply

> 1) allowing the user to specify a separator with a header argument as
>    follows
>    #+begin_src sh :var table=sec :separator ,
>      cat <<EOF
>      $table
>      EOF
>    #+end_src
>    
>    which would result in something like
> 
>    : "Hello, World"

I like this idea because it is what I would expect. In my first
"experiment", I assumed that I can use the "|" as a separator. I would
like to use a table as input form and pipe the rows to a shell script
written in org-babel. Sometimes it is easier to proccess data with
awk instead of using elisp. So my example is a bit misleading.

> 2) writing the table to a tab or comma separated file and then
>    replacing =$table= in the source block body with the path to the
>    file name, s.t. something like

IMHO it is not necessary under Unix. Reading from stdin is usual. But it
maybe different under Windows.

Many thanks
Matthias

Re: Passing a table to org-babel shell script

[Eric Schulte]

Alright,

I've set this up so that the table is exported to a comma or tab
separated format and then saved as a string to the variable in the
source code block.  By default tab is used as the separator when
exporting the table to a string, but this can be overridden using
the :separator header argument.

The following large snippet show some example usage of tables in shell
scripts.  Please let me know how it works for you and if you have any
other suggestions.

Thanks -- Eric

--8<---------------cut here---------------start------------->8---
#+tblname: fibs
| 1 | 1 |
| 2 | 1 |
| 3 | 2 |
| 4 | 3 |
| 5 | 5 |
| 6 | 8 |

#+begin_src sh :var table=fibs
  echo "$table" |wc
#+end_src

#+results:
: 6      12      24

#+begin_src sh :var table=fibs
  echo "$table"
#+end_src

#+results:
| 1 | 1 |
| 2 | 1 |
| 3 | 2 |
| 4 | 3 |
| 5 | 5 |
| 6 | 8 |

#+begin_src sh :var table=fibs :separator --
  echo "$table" | head -1
#+end_src

#+results:
: 1--1
--8<---------------cut here---------------end--------------->8---


Matthias Teege <matthias-omd@mteege.de> writes:

> On 11:33 Sat 06 Feb, Eric Schulte wrote:
>
> Moin,
>
> thanks for your reply
>
>> 1) allowing the user to specify a separator with a header argument as
>>    follows
>>    #+begin_src sh :var table=sec :separator ,
>>      cat <<EOF
>>      $table
>>      EOF
>>    #+end_src
>>    
>>    which would result in something like
>> 
>>    : "Hello, World"
>
> I like this idea because it is what I would expect. In my first
> "experiment", I assumed that I can use the "|" as a separator. I would
> like to use a table as input form and pipe the rows to a shell script
> written in org-babel. Sometimes it is easier to proccess data with
> awk instead of using elisp. So my example is a bit misleading.
>
>> 2) writing the table to a tab or comma separated file and then
>>    replacing =$table= in the source block body with the path to the
>>    file name, s.t. something like
>
> IMHO it is not necessary under Unix. Reading from stdin is usual. But it
> maybe different under Windows.
>
> Many thanks
> Matthias
>
>
>
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