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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: A few questions before choosing Taverna for our project
Date Tue, 31 Mar 2015 11:05:17 GMT
No, you should not need to touch Baclava at all :)

You will need to retrieve the provenance bundle separately once the
run has finished. It should be available at .../run-bundle in the REST
API:

http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle

On 31 March 2015 at 11:34, Ahmad Aburomman <ahmad.aburomman@rai.usc.es> wrote:
> Thanks a lot for your indeed reply, actually I'm using this project
> https://github.com/pgcc/taverna-java-client
>
> I have implemented the Provenance function in TavernaClient.java, it is okay now and
enabled but still can't get the provenance data with the output
> You mentioned that I have to do some function to Baclava, can you guide me please or
give me the exact script to update my project.
>
> Regards
> Ahmad
>
> -----Original Message-----
> From: Stian Soiland-Reyes [mailto:stain@apache.org]
> Sent: Friday, March 27, 2015 2:24 PM
> To: users@taverna.incubator.apache.org
> Subject: Re: A few questions before choosing Taverna for our project
>
> Not sure where you found that code, as I found they were implemented here:
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L344
>
>
> but in either case, the baclava input/output should NOT be used if you want the workflow
run bundle back.
>
>
> Unfortunately the Taverna Server client code for Java has not been updated for the run
bundle, which was new in 2.5 I think.
>
> It would be great if you could have a quick go - I think it should be quite doable, we've
just not got around to it yet...
>
> Use the 'next' branch from https://github.com/myGrid/t2-server-jar/
>
>
> By
> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/generate-provenance
> you need to send a PUT with "true" to /runs/{id}/generate-provenance
>
> so perhaps something like this could work?
>
>
> package uk.org.taverna.server.client.Run add two new methods, e.g.:
>
> similar to isBaclavaOutput and requestBaclavaOutput
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L404
>
> but with "generate-provenance" added to the run URL.
>
>
> Similarly add  getRunBundle() similar to getOutputZip()
>
> https://github.com/myGrid/t2-server-jar/blob/next/src/main/java/uk/org/taverna/server/client/Run.java#L1140
>
> .. but requesting "run-bundle" added to the URL.
>
>
> To do it "proper REST-like" this can be generalized to find those two URI fragments from
the runDescription as you see with getLink() in other bits of the code.
>
> On 27 March 2015 at 12:07, Ahmad Aburomman <ahmad.aburomman@rai.usc.es> wrote:
>> Yes I see these code about baklava, but I don't know what to add exactly!
>>
>> @Override
>>     public String getBaclavaInput(String uuid) throws TavernaException {
>>         throw new UnsupportedOperationException("Not supported yet."); //To change
body of generated methods, choose Tools | Templates.
>>     }
>>
>>     @Override
>>     public String setBaclavaInput(String uuid, String file) throws TavernaException
{
>>         throw new UnsupportedOperationException("Not supported yet."); //To change
body of generated methods, choose Tools | Templates.
>>     }
>>
>>
>>     @Override
>>     public void setBaclavaOutput(String uuid, String file) throws TavernaException
{
>>         throw new UnsupportedOperationException("Not supported yet.");
>>
>>
>>
>> -----Original Message-----
>> From: Stian Soiland-Reyes [mailto:stain@apache.org]
>> Sent: Friday, March 27, 2015 12:28 PM
>> To: users@taverna.incubator.apache.org
>> Subject: Re: A few questions before choosing Taverna for our project
>>
>> I think it should suffice in the client - although you might have to add support
for it in the java client as the generate-provenance option was added recently.. Would you
be willing to have a go at that?
>>
>> On 27 March 2015 at 11:08, Ahmad Aburomman <ahmad.aburomman@rai.usc.es> wrote:
>>> Okay, that seems to edit or modify some scripts, but which file should I do this?
Inside Taverna server directory or in the java client?
>>> Please explain more
>>>
>>> Thanks
>>>
>>> -----Original Message-----
>>> From: alaninmcr [mailto:alaninmcr@googlemail.com]
>>> Sent: Thursday, March 26, 2015 9:03 PM
>>> To: users@taverna.incubator.apache.org
>>> Subject: Re: A few questions before choosing Taverna for our project
>>>
>>> On 26/03/2015 19:45, Ahmad Aburomman wrote:
>>>> Dear Stian,
>>>>
>>>> I'm working on workflow and I ran it perfectly (tomcat6 and
>>>> RESTful), I got the output without provenance bundle
>>>
>>> Before you started the run, did you set generate-provenance to true?
>>>
>>> Also, you need to make sure you are not sending the outputs to a Baclava file.
>>>
>>> See
>>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resourc
>>> e
>>> :/runs/{id}/generate-provenance
>>>
>>>> I don't know how to configure Taverna server to enable provenance
>>>> data, can you guide me please?
>>>
>>> It is not part of the server configuration. It is set for each run.
>>>
>>>> Kind regards
>>>>
>>>> Ahmad
>>>
>>> Alan
>>>
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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