[MOBY-dev] Parse_moby_data processor in taverna fails

[Arnaud Kerhornou]

Hi,

I just tried a workflow that was working fine last week with taverna 
1.6.2.1, and it gets stuck on the parse_moby_data stage (See the 
exception stack below),

(I have attached the workflow, it takes a fasta sequence)

Can someone look into this, please ?

Thanks
Arnaud

PS:
Taverna Exception stack:

WARN  2007-11-26 11:19:51,714 There was a problem writing to the cache:
org.biomoby.shared.MobyException: Cannot write to 
'/Users/axk/Library/Application 
Support/Taverna-1.6.2/moby-cache/http58.47.47mobycentral46icapture46ubc46ca47cgi45bin47MOBY0547mobycentral46pl/service_rdf/SERVICE_INSTANCE.rdf'. 
java.io.IOException: Server returned HTTP response code: 500 for URL: 
http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances
        at 
org.biomoby.client.taverna.plugin.CacheImpl.storeURL(CacheImpl.java:363)
        at 
org.biomoby.client.taverna.plugin.BiomobyScavengerWorker.updateServiceInstanceCache(BiomobyScavengerWorker.java:742)
        at 
org.biomoby.client.taverna.plugin.BiomobyScavengerWorker.getServices(BiomobyScavengerWorker.java:392)
        at 
org.biomoby.client.taverna.plugin.BiomobyScavenger.<init>(BiomobyScavenger.java:50)
        at 
org.biomoby.client.taverna.plugin.BiomobyScavengerHelper.getDefaults(BiomobyScavengerHelper.java:140)
        at 
org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool$ScavengerHelperThread.run(ScavengerHelperThreadPool.java:123)
Cannot parse MOBY Object Ontology: java.lang.NullPointerException
java.lang.NullPointerException
        at 
org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:182)
        at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:88)
        at 
org.biomoby.shared.data.MobyDataComposite.<init>(MobyDataComposite.java:35)
        at 
org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:186)
        at 
org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:152)
        at 
org.biomoby.shared.data.MobyContentInstance.parseDataGroup(MobyContentInstance.java:240)
        at 
org.biomoby.shared.data.MobyContentInstance.<init>(MobyContentInstance.java:125)
        at 
org.biomoby.shared.data.MobyDataUtils.fromXMLDocument(MobyDataUtils.java:93)
        at 
org.biomoby.shared.data.MobyDataUtils.fromXMLDocument(MobyDataUtils.java:48)
        at 
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType(ParseMobyXML.java:75)
        at 
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute(MobyParseDatatypeTask.java:100)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
        at 
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67) 



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