Re: ePCR fetch

[Andreas Tille <tille@debian.org>]

Hi Saira,

On Mon, Jun 24, 2019 at 02:20:29PM +0100, Saira Hussain wrote:
> I pushed towards the master my python script to be used for fetching data
> from the database in order to be further modified and used for testing of
> the ePCR package.

I confirm your fetch_fasta.py script works (=creates a data file).  I've
added a #! line on top which is more convenient since you can call the
script directly.
 
> I have one problem down the line, as ePCR isn't happy with my final
> converted file but I am working on it.

Could you please specify your problem?  What command line are you
calling and what is the output of this command?  What error is
happening?
 
> Meanwhile could you give me some feedback? I hope a Python script is fine as
> it's quite comfortable for me to write Python.

This script is not yet the test for ePCR - it just *documents* how the
used data are obtained.  In other words: You can write your
documentation in whatever language you want (some comment in the header
what this script is doing and why the data are fetched that way would be
helpful).
 
> Could I write further tests in Python instead of sh or bash scripts are
> preferred?

In principle the tests can be written in any language but I admit I do
not see a big need for it.  In all tests written for Debian Med
maintained packages shell was perfectly sufficient and we have a very
frequently used template[1] where you usually simply add a program call.
I'd consider a Python script unnecessary overkill and you should provide
more reasons why you think in this case some higher level language would
be better.
 
> Looking forward to your comments and suggestions,

Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/community/package_template/blob/master/debian/tests/run-unit-test 

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