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From "Ahmad Aburomman" <ahmad.aburom...@rai.usc.es>
Subject RE: A few questions before choosing Taverna for our project
Date Thu, 26 Mar 2015 19:45:01 GMT
Dear Stian,

I'm working on workflow and I ran it perfectly (tomcat6 and RESTful), I got the output without
provenance bundle

I don't know how to configure Taverna server to enable provenance data, can you guide me please?


 

Kind regards 

Ahmad

-----Original Message-----
From: Matthieu Melcot [mailto:matthieu.melcot@spaceapplications.com] 
Sent: Tuesday, March 24, 2015 12:50 PM
To: users@taverna.incubator.apache.org
Subject: Re: A few questions before choosing Taverna for our project

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,

Matthieu



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+dis
> covery+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/s
> rc/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLS
> plitterAction.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-td402499
>> 7.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#Result
> Perspective-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 www.spaceapplications.com


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