[MOBY-dev] Executing Moby Workflow straight from java
Sergio Ramirez Ramirez
srramirez at uma.es
Thu Sep 25 10:29:18 UTC 2008
Yes, you are right but taverna still using it in the core.
If you download the entire src of taverna you will find a jar file:
taverna-workbench with that class
If you couldn't find it, just tell me and I will sent it to you
Best regards, Sergio
Jerzy Orlowski wrote:
> 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 I have an impression that freefluo is outdated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
>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> 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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--
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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