[MOBY-dev] Parse_moby_data processor in taverna fails

[Arnaud Kerhornou]

hi Eddie,

Actually the taverna workflow worked but I still get an Exception
at the moby parsing stage.

Should I clean my local cache ?

Arnaud

PS: Exception stack
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: 502 for URL: 
http://mobycentral.icapture.ubc.ca/authority/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:709)
        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)

Edward Kawas wrote:
> Hi Arnaud, 
>
> It seems to be working now. Not sure what the problem was, but I just ran
> your workflow with your inputs and it worked for me.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Arnaud Kerhornou
> Sent: November-26-07 3:27 AM
> To: 'Core developer announcements'
> Subject: [MOBY-dev] Parse_moby_data processor in taverna fails
>
> 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 it, please ?
>
> Thanks
> Arnaud
>
> 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/http58.47.47mobycentral46icapture46ubc46ca4
> 7cgi45bin47MOBY0547mobycentral46pl/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.updateServiceInstan
> ceCache(BiomobyScavengerWorker.java:742)
>         at 
> org.biomoby.client.taverna.plugin.BiomobyScavengerWorker.getServices(Biomoby
> ScavengerWorker.java:392)
>         at 
> org.biomoby.client.taverna.plugin.BiomobyScavenger.<init>(BiomobyScavenger.j
> ava:50)
>         at 
> org.biomoby.client.taverna.plugin.BiomobyScavengerHelper.getDefaults(Biomoby
> ScavengerHelper.java:140)
>         at 
> org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool$ScavengerH
> elperThread.run(ScavengerHelperThreadPool.java:123)
> Cannot parse MOBY Object Ontology: java.lang.NullPointerException
> java.lang.NullPointerException
>         at 
> org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeP
> arser.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(MobyContentInstan
> ce.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(ParseMo
> byXML.java:75)
>         at 
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute(MobyParseDat
> atypeTask.java:100)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenera
> teTemplates(ProcessorTask.java:576)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocation
> WithRetryLogic(ProcessorTask.java:517)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(P
> rocessorTask.java:436)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithou
> tIteration(ProcessorTask.java:642)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(Proce
> ssorTask.java:353)
>         at 
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(Pr
> ocessorTask.java:280)
>         at 
> uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
>
>
>
>   


	
	
		
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