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From Matthieu Melcot <matthieu.mel...@spaceapplications.com>
Subject Re: A few questions before choosing Taverna for our project
Date Tue, 24 Mar 2015 11:50:27 GMT
Dear Stian,

Thank you for the answer, and the time you spent to give us details 
about Taverna specific points. It helped a lot!

We keep on testing Taverna, and I will come to you if I have other 
specific questions.

Best regards,


On 2015-03-02 14:06, Stian Soiland-Reyes wrote:
> Hi! Great that you are considering Taverna!
> On 27 February 2015 at 10:30, Matthieu Melcot
> <matthieu.melcot@spaceapplications.com> wrote:
>> The core of the project is the orchestration of WPS processes
>> (http://www.opengeospatial.org/standards/wps) which are Web Services for
>> Geospatial processing.
>> Basically, a client can request one of the 3 following "GetCapabilities",
>> "DescribeProcess", "Execute" and get a
>> response in XML
> Great! Others here have already been using Taverna with WPS services -
> I know Alan Williams has some experience as well:
> http://markmail.org/message/y4elmrinjlyseoc4
>> The WPS server implementation that we will use
>> (http://52north.org/communities/geoprocessing/wps/) doesn't embed the WPS
>> xml inside SOAP (even if the OGC WPS norm describes it), and their are not
>> WSDL capabilities.
> But it does expose a SOAP/WSDL endpoint? Then it should in theory work
> out of the box - even though you would have to deal with the "service
> through a service" pattern of the generic DescribeProcess/ Execute
> calls.
>> 1) Is it relatively easy to develop a component for Taverna that will allow
>> to add these WPS services into the "Services Available" for building a
>> workflow ? Which kind of effort would it represent ?
> It's fairly easy to add a new Services Available plugin - see the Tutorial here:
> http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin
> Note that this tutorial is relevant for Taverna 2.5 , the upcoming
> Apache Taverna 3 would have slightly different ways of creating
> activities in the workbench.
> A service discovery module is allowed to return existing services
> (e.g. WSDL Activity) and don't have to create their own activity types
> (although the tutorial returns the HelloWorld type of activities)
> Note that creating WSDL activities programmatically could be slightly
> complicated if you need to add XML splitters for inputs and outputs -
> which I believe is needed for. You can have a look at the wsdl
> activity UI code for "Add XML splitter" for inspiration - See the
> Taverna 2 code here:
> https://github.com/taverna/taverna-wsdl-activity-ui/blob/maintenance/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
> (Dmitry might have inputs on alternative ways to do this in Taverna 3
> - but for now I think you should target the Taverna 2 workbench as
> Apache Taverna 3 workbench probably won't be released before Q3 2015)
> A tighter integration with a "WPS Activity" plugin could give a much
> smoother expirence for the workflow design user, as you could expose a
> single step that interrogates the WPS server for input and output
> parameters and present these directly in Taverna as ports - this would
> take some more time - but has been done for many similar kind of
> service-in-a-service cases for Taverna, e.g. the Soaplab Activity.
> We did something similar when we created the AstroTaverna plugin for
> Taverna - but ended up making a new Perspective to have a richer
> search interface against the VO service registry -
> http://amiga.iaa.es/p/290-astrotaverna.htm
> Here the perspective allow a rich way to search and display
> information about VO compliant REST services, and then adding them to
> the workflow and/or Service Panel with a button.
>> I read
>> (http://geoprocessing.forum.52north.org/Problem-with-Taverna-td4024997.html)
>> that some people try to use WPS with Taverna (Through WSDL however), but
>> they didnt succeed.
> Alan might be able to fill me in - but I believe this is mainly caused
> by an incomplete
> WSDL created by the WPS server.
>> 2) In the case that it is possible, is there some possibilities to describe
>> semantically the input and output of these WPS services (indeed the input
>> and outputs will always be URL (texts), but the URLs reference different
>> types of materials), so that it would be possible to check if the
>> connections are valid. It seems that Taverna has that kind of mechanism...
> Taverna does not have that kind of mechanism directly, but it is not
> far off from being able to do so. The main problem is the source of
> the semantic type annotations - a source like WPS service descriptions
> would be a good candidate.
> Mark Fortner has also shown interest in adding such a mechanism:
> http://markmail.org/message/zhmas3ifgmzccdsj
>> 3) My third question is about the monitoring and control of the workflow
>> execution.
>> Is there a way through the REST API to ask which part of a workflow is
>> actually executing.
> Not yet - but that is the plan as we are moving Taverna Server 3 to
> use the Taverna Platform directly instead running the engine through
> the command line.
> We will then be able to expose the workflow run report, which is a
> JSON document that details all processors and what they are doing,
> have done and still remains to do. Basically a detailed data structure
> similar to the Progress table at
> http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective#ResultPerspective-ProgressReport
> You could access this today, but only through the Java API of the Engine.
>> 4) Is there a simple Web Viewer/Controller (It seems that the "Taverna
>> Player" needs to be embedded in web pages in ruby). Is there a more
>> straightforward way to use this player in order to test it ?
> Yes, Rob Haines and Finn Bacall made this basic portal so you won't
> have to make your Ruby portal to try it out:
> https://github.com/myGrid/taverna-player-portal
>> 5) Is there a mean to control and monitor the execution of a remote workflow
>> directly from the Taverna Workbench. It seems that "File / Open Workflow
>> Location" makes reference to a .t2flow remote file, and not a workflow that
>> would have been load into the Taverna Server.
> Not yet - but that is the goal of making the Taverna Platform binding
> to the Taverna Server API - the Taverna 3 workbench has the separation
> so that this is in theory easy. The main thing it is missing is that
> very same JSON report, which needs to be added also to the client
> code.
> Some simple UI code would also be needed to "Add your server".
> As an Apache project with open development, anyone can contribute to
> the development of Taverna.
> Do you think you (or your team) would be able to help out with
> updating and testing the Taverna Server for such an integration?
> For instance I think we need to clarify what should be the granularity
> of the report, how to deal with refreshing, loading intermediate data,
> etc.

Matthieu Melcot
Software Engineer

Space Applications Services NV/SA
Leuvensesteenweg 325, 1932 Zaventem, Belgium
Direct: +32-(0)2-416.05.35
Main: +32-(0)2-721.54.84 Fax: +32-(0)2-721.54.44

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