[MOBY-dev] Executing Moby Workflow straight from java

[Jerzy Orlowski]

I keep trying, but I cannot find anywhere a jar with
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser

I have an impression that freefluo is outdated

----------------------------------------------------------------------
uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error 
with configuration named tavernaClassNotFound for WorkflowParser 
implementation: 
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
	at 
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108)
	at 
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.<init>(EngineConfigurationImpl.java:64)
	at org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84)
	at org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11)
Caused by: java.lang.ClassNotFoundException: 
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at 
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102)
	... 3 more
------------------------------------------------------------------------

Jerzyo



Sergio Ramirez Ramirez wrote:
> Hi Jerzy
> 
> I see you cannot got to resolve the problem.
> 
> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel;
> 
> Maybe is what you need. to built your own workflow.
> 
> Keep me informed ;) and good luck.
> 
> Jerzy Orlowski wrote:
>> Hi
>>
>> I am trying to use your code, but I get strange erros like:
>>
>> The constructor EngineImpl(EngineConfiguration) is undefined
>>
>> Perhaps I am working on different versions of the code (some from 
>> taverna, some from ogasadai and some from freefluo).
>>
>> Where can I find source code or javadoc for 
>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other 
>> classes?
>>
>> I cannot find in anywhere on the web....
>>
>> Jerzy
>>
>>
>> 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
>>>>>>
>>>>>
>>>>>
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>>>
>>>
>>
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> 
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