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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: GSOC: Add Common Workflow Language support to Taverna
Date Wed, 21 Feb 2018 11:57:32 GMT
Hi, Majdi, thank you for your intest in GSOC and Apache Taverna!
Apologies for late reply.

On Thu, 15 Feb 2018 05:08:55 +0100, Majdi Haouech <majdi.haouach@gmail.com> wrote:
> I have worked with different languages and technologies, to name a few:
> Java, C, C++, Python, JS, Git, OWL, JavaEE, RabbitMQ, Maven.
> I am also contributing to a Mozilla open source project which required
> working with existing code and delivering a full working and completely
> tested contribution.

This is a strong background!  It's good you have experience with both
OWL, Python and Java.   As you might have noticed the cwltool reference
implementation is written in Python, while Taverna is (largely) in Java.

> > First, I need to be familiar with the CWL specification in order to be able
> > to convert YAML files to Taverna workflows.
> > Next, I'll need to do the opposite work by transforming a Taverna workflow
> > into YAML files following the CWL specification as well.
> > Finally, if there will be enough time, I can contribute to Taverna's Tool
> > Activity by completing the TAVERNA-878 issue.
> > I understand that the contribution will be to the Taverna Language API and
> > any other remarks are welcome.

Yes, this can be a good way to start.  I am a bit worried about going
for both CWL import and export at the same time - although trying to
have some kind of round-trip support would be wonderful!

I think what you are proposing is to keep the translation structural at
first, that is Taverna can import the CWL workflow and get the 
correct boxes/arrows connected, but would not know
how to execute the CWL tools (pending TAVERNA-878).   

So this could for instance be that you import CWL tools into the dummy
CWL activity we already have 
where it would just keep a JSON tree of the CWL Tool configuration
without knowing how to execute it.  That should make it easier to do a
round-trip save out again.

TAVERNA-878 could easily also be the most time-consuming part of the
effort, so it might be good to not risk all on that.  You may have a go
at doing just simple CWL command line tools (e.g. just arguments and
stdin/out without files) which should be easier to map to the existing
Tool activity.

Export of Taverna Workflows to CWL can seem challenging because in
Taverna we have many types of activities which are not supported by
other CWL engines:

So again it could be a structural export where the CWL side just has
"TavernaActivity" and includes the Taverna Activity JSON for opposite
round-trip, but would not be executable on other CWL engines.

(They should however work on http://view.commonwl.org/)

If you then towards the end want to move beyond structural/skeleton
export of Taverna workflows into CWL  you can progress to export the
Taverna's Command Tool activity as CWL command line tools. Again there
might be features in the Taverna side that don't match exactly to CWL,
which you can say is not supported.

> > I am used to work with different technologies and dealing with different
> > specifications.

Great, yes, that is perhaps also the greatest challenge of this
particular GSOC project, in that you will be integrating between several
existing technologies and specifications!

> > I am also used to work with existing code and extending it.
> > Also, I am really motivated for contributing to an Apache project and this
> > opportunity is perfect for me to dive right in with the right support.

Thank you, we very much welcome your effort! 

What I think you could do next is to have a go with the different
technologies, see the tutorials - and then start building a proposal
(Google Docs?) where you list the background material and 
start listing your task breakdown.

Taverna Language has some (but not much) doc at 

The GOSC proposal is due mid March so there is time to develop it now -
but it's good if you keep in touch with us at dev@taverna so we can 
review it before the deadline; we want GSOC to be successful as well!

Stian Soiland-Reyes
The University of Manchester

Stian Soiland-Reyes

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