[MOBY-dev] Executing Moby Workflow straight from java

[José María Fernández González]

Hi everybody,
	as Sergio *should* know, we have at INB IWWE&M, which means 'Interactive Web 
Workflow Enactor and Manager'. It is able to host workflows, workflow examples 
with documentation, do web workflow enactions, and take and store workflow 
enaction snapshots.

	Next days we are going to have a Trac server with is going to host the source 
code and development of IWWE&M.

	Best Regards,
		José María

Sergio Ramirez Ramirez wrote:
> 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
>>>>
>>>
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

José María Fernández González
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinformática
Biología Estructural y Biocomputación	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fernández Almagro, 3	Madrid (Spain)

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.