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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Check consistency between baclava and t2flow
Date Tue, 15 Mar 2016 17:38:13 GMT
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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