taverna-users mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Stian Soiland-Reyes <st...@apache.org>
Subject Re: A few questions before choosing Taverna for our project
Date Tue, 31 Mar 2015 11:03:20 GMT
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


Ah, that code is brand new to me and seems to be written for Taverna
Server 2.5 - we should invite Vitor to join the mailing list.


Vitor - Ahmad here have some questions about your taverna-java-client
and getting the provenance back
http://markmail.org/message/gplybw7ruvgef6o7

I was confused as I thought he was talking about
https://github.com/myGrid/t2-server-jar/
.. which has not been updated for Taverna 2.5 -- your code is made
from scratch against the 2.5 APIs, right?



Vitor, have you signed up to the Apache Taverna mailing lists? We
would love to have you on board and possibly join effort on the
Taverna Server client effort! Also it would be cool to hear what you
use Taverna for.

http://taverna.incubator.apache.org/contact/

> 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

Mime
View raw message