HI ,
Thanks for quick response.I am Thilina Manamgoda third year undergraduate
of Computer Engineering ,University of Peradeniya.I live in town called
Matale in Sri Lanka.This our faculty web site :http://www.ce.pdn.ac.lk/ .I
have done IOT backend server project in my short semester and several other
projects selected by myself.You can see them here:
https://github.com/ThilinaManamgoda.I am comfortable with languages like
JAVA,C,NODEJS,JAVASCRIPT .When i am doing projects which i mentioned early
,i have engaged with JSON concepts.
I already going through Getting
Started documentation for Taverna and joined CWL community discussion on
https://gitter.im/common-workflow-language/common-workflow-language to get
better idea about their concepts.But i still in early stage
of understanding these concepts .So i am going to come up with lot of
questions soon.
Regards,
Thilina.
On Sun, Feb 28, 2016 at 7:30 AM, Stian Soiland-Reyes <[email protected]>
wrote:
> Hi, thanks for showing early interest!
>
> Perhaps you would like to tell us a bit about yourself and your background?
> Are you studying Computer Science?
>
> First of all you probably want to have a quick look at the Getting Started
> documentation for Taverna, and try the Taverna Workbench Core 2.5 download.
> There should be a tutorial for building a hello world workflow somewhere,
> I'll see if I can find it.
>
> Basically what this task you mention is about is to add support for finding
> CWL tools under the top-left Available Services panel, so they can be
> dragged into the workflow.
>
> The remaining tasks deal with how to execute such CWL tools, and how to
> represent a Taverna workflow in CWL (or vice versa)
>
> The Jira issue gives an introduction and various links to related material.
>
> As for the Workbench integration we have already this plugin developer
> tutorial:
>
>
> http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin
>
> Unfortunately this tutorial relates to Taverna 2, while now we develop
> Taverna 3. Naturally we would hope for your potential contribution to apply
> to Taverna 3, which has a slightly different mechanism for Taverna Activity
> configuration (JSON object instead of a Java Bean).
>
> We have not yet released the Taverna 3 Workbench, so testing your work
> might require other modifications to the T3 Workbench code to get it
> running. We would appreciate any general fixes there (e.g. if we have the
> wrong import statements after moving to org apache.taverna) - but it could
> be sufficient for you to track such issues and discuss them on our mailing
> list
>
> However for your discovery side I think it should be fine for you to start
> work in Taverna 2 and with a dummy Activity that just keeps a Jackson JSON
> object, and then adapting your code to Taverna 3 would be a nice second
> phase.
>
> As for discovery side this is still early days in the CWL community, so you
> want to engage them to ask what are the plans for a tool registry. I know
> they are working with the http://bio.tools/ guys, but I am not sure how
> easy it is to add CWL Tool YAML/JSON directly there (or by reference).
>
> As far as I've seen CWL used, each tool is typically stored in a separate
> YAML file. Perhaps a good start is to just "discover" within a fixed or
> configured directory which we can populate manually with from CWLs Github
> examples.
>
> The Service Discovery mechanism in Taverna can do searches over fields, so
> an add-on task could be to expose some of the metadata that could be in the
> tool description, e.g. function:sequencing. However I think again metadata
> work in CWL is early days and you might need to work with the CWL community
> to get good examples.
> On 27 Feb 2016 12:23, "Thilina Manamgoda" <[email protected]> wrote:
>
> > Hi,
> >
> > I am interested in "Browse and use CWL tool descriptions from the
> > workbench" task and to get better idea about this project can you
> provide
> > me a guide line please.
> >
> > Regards
> > ,Thilina
> >
> > On Sat, Feb 27, 2016 at 4:40 PM, Alan Williams <[email protected]
> >
> > wrote:
> >
> > > On 27-Feb-16 09:05, Thilina Manamgoda wrote:
> > >
> > >> HI,
> > >>
> > >
> > > Hello
> > >
> > > Source: https://issues.apache.org/jira/browse/TAVERNA-900
> > >>
> > >> I am Thilina Manamgoda undergraduate from University of Perandeniya. I
> > >> would like to contribute this project for GSOC 2016.
> > >>
> > >
> > > That is great.
> > >
> > > In order to add CWL support to Taverna following steps should be
> taken.
> > >>
> > >> 1.Save Taverna workflows as CWL
> > >> 2.Read CWL workflows
> > >> 3.Execute CWL tool descriptions
> > >> 4.Browse and use CWL tool descriptions from the workbench
> > >> 5.Create a Docker tool for executing Taverna activities
> > >>
> > >> So for Gsoc 2016 i need to get better idea about the project ,am i
> > >> supposed
> > >> to do one of above task or all of them ?.
> > >>
> > >
> > > As the issue says, "the GSOC student can ... choose to pursue one or
> two
> > > of these tasks in detail"
> > >
> > > So, if you are interested in (for example) Docker, you might want to
> > > concentrate on #5.
> > >
> > > As part of a submission to become a GSOC student, you do a proposal of
> > > what you plan to do. That proposal will depend on which task(s) you are
> > > interested in working on. The content of a proposal from someone
> > interested
> > > in #1 would be very different to that for someone working on #4.
> > >
> > > Which task(s) are you interested in?
> > >
> > > Feel free to ask as many questions as you want.
> > >
> > > Regards,
> > >> Thilina.
> > >>
> > >
> > > Alan
> > >
> > >
> >
>
