[MOBY-dev] Executing Moby Workflow straight from java

[Sergio Ramirez Ramirez]

Here there is my small contribution, just the two methods that I use for 
run a workflow.
Hope it can help to someone

Paul Gordon wrote:
> I think whoever has a headless Taverna workflow creation and/or 
> enactment working should put examples up in the Java developer's 
> section of the Moby Web site...I believe the myExperiment people also 
> have a headless workflow enactment engine working now...anyone from 
> there on this list?  Also, Paolo Romano in Italy has a headless SCUFL 
> enactor in the BioWEP software. So many people are doing this, but no 
> good sample code is easily available, especially for Moby services...
>
> Sergio Ramirez Ramirez wrote:
>> Hello Jerzy
>>
>> I had the same problem that you.
>>
>> I have got it to work by browsing deep in the Taverna code. I cannot 
>> give you many sample code because I'm trying to organize all the code 
>> tries and examples that I have.
>>
>> But I can give you some comments:
>>
>> For build a workflow model the class is: 
>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = 
>> new ScuflModel();
>> This class contains the methods that you mention addProcessor ...
>>
>> For run I'm using freeflow, because taverna classes and raven are a 
>> "little" tricky. The classes:  
>> uk.ac.soton.itinnovation.freefluo.main.Engine or 
>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy 
>> can help you.
>>
>> I hope this little details help you to begin. If you have more 
>> detailed questions I will be very happy of help you.
>>
>> Best regards,
>> Sergio
>>
>> Jerzy Orlowski wrote:
>>> Hi
>>>
>>> I have several hundreds of workflows made up of BioMoby Services and 
>>> want to execute them all without opening any GUI.
>>>
>>> I was looking for some solution over the internet and the think I 
>>> came across was using Taverna plugin and try to execute it 
>>> programaticaly.
>>> I have a few questions:
>>>
>>> 1. Is it the only way?
>>>
>>> 2. I found several tutorial tutorials on running  saved workflow 
>>> saved in scufl language.
>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html 
>>>
>>>
>>> How do you one make a workflow step by step? like:
>>>
>>> workflow.addProcesor(...)
>>> workflow.addConnector(...)
>>> ...
>>> workflow.execute()
>>>
>>> and especially, how do one add BioMoby objects this way? Is there 
>>> any tutorial or do I have go though the API?
>>>
>>> Best
>>>
>>> Jerzy Orlowski
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>
>>
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-- 
Sergio Ramírez Ramírez
Instituto Nacional de Bioinformática (INB)
Integrated Bioinformatics Node (GNV-5)
Dpto. de Arquitectura de Computadores
Campus Universitario de Teatinos, despacho 2.3.9a
29071 Málaga (Spain) +34 95 213 3387


"Short-term decisions tend to fail in the long-term."
            Frank Herbert, God Emperor of Dune 

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