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From Ian Dunlop <ianwdun...@gmail.com>
Subject Re: Check consistency between baclava and t2flow
Date Tue, 15 Mar 2016 19:39:53 GMT
Hello

@stian That's a really useful answer that we should add to a FAQ somewhere.
Also sounds like a possible gsoc to "Apache taverna-ise" the server. Maybe
too late now though.

Cheers

Ian
On 15 Mar 2016 5:38 pm, "Stian Soiland-Reyes" <stain@apache.org> wrote:

> You can ask the REST API what the expected input ports are by calling:
>
>  /runs/{id}/input/expected
>
> See
>
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/input/expected
>
>
> However I don't think uploading a baclava is validated in any way by
> Taverna Server (perhaps that should be a bug?), so currently I think
> you would have to parse the baclava file yourself to see if the top
> level map matches the input keys. Ideally validation would need to
> check the list depths as well.
>
>
> You can use the taverna-baclava-language module from Apache taverna
> language to parse the Baclava file:
>
>
> http://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/baclava/BaclavaReader.html
> https://taverna.incubator.apache.org/download/language/
>
> using: <artifactId>taverna-baclava-language</artifactId>
>
>
> Perhaps the Taverna Server Baclava upload could be improved to use
> taverna-baclava-language and do such validation?
>
> Relevant source:
>
>
> https://github.com/apache/incubator-taverna-server/blob/master/taverna-server-webapp/src/main/java/org/taverna/server/master/InputREST.java#L113
>
> https://github.com/apache/incubator-taverna-server/blob/master/taverna-server-webapp/src/main/java/org/taverna/server/master/InputREST.java#L88
>
> https://github.com/apache/incubator-taverna-server/blob/master/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/RemoteRunDelegate.java#L356
>
> https://github.com/apache/incubator-taverna-server/blob/master/taverna-server-worker/src/main/java/org/taverna/server/localworker/impl/LocalWorker.java#L625
>
>
> On 15 March 2016 at 13:47, Simone Bnà <s.bn@cineca.it> wrote:
> > Dear Ian,
> >
> > I am using the taverna server 2.5.4.
> > In attachment you find the t2flow and baclava I used to find the issue.
> > In taverna workbench I don't find any issues since in the baclava
> loading interface
> > you cannot load a inconsistent baclava respect to the t2flow you are
> using.
> >
> > Best regards,
> >
> > Simone.
> >
> > ----- Original Message -----
> > From: "Ian Dunlop" <ianwdunlop@gmail.com>
> > To: users@taverna.incubator.apache.org
> > Sent: Tuesday, March 15, 2016 12:17:09 PM
> > Subject: Re: Check consistency between baclava and t2flow
> >
> >
> > Hello,
> >
> >
> > Hi Simone, thanks for reporting the issue. Could you attach the workflow
> that was causing issues. Which version of Taverna are you using. Are you
> using the desktop app or the server?
> >
> >
> > Cheers,
> >
> >
> > Ian
> >
> >
> > On 15 March 2016 at 10:47, Simone Bnà < s.bn@cineca.it > wrote:
> >
> >
> > Hi all,
> >
> > I experienced a problem when running a workflow with an inconsistent
> baclava.
> > Let me explain better:
> > If I submit a workflow to Taverna with a set of input ports which are
> different from the ones described in the baclava,
> > taverna does not complain but the run will never terminate.
> > Is there a way to check the consistency between a t2flow workflow and
> the baclava?
> >
> > Best regards,
> >
> > Simone.
> >
> > --
> > Simone Bnà, PhD
> > C++ Software Developer, CINECA
> > Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
> > office: +39-0516171938
> > email: s.bna@scsitaly.com/s.bn@cineca.it
> >
> > --
> > Simone Bnà, PhD
> > C++ Software Developer, CINECA
> > Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
> > office:   +39-0516171938
> > email: s.bna@scsitaly.com/s.bn@cineca.it
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>

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