[MOBY-dev] Parse_moby_data processor in taverna fails

[mark wilkinson]

Hi all,

I have a feeling that these problems were largely rooted in the fact that the LSID resolver caches its WSDL.  When I was testing things against the new code against the new endpoint this weekend I was using the LSID resolver on MobyCentral, and it seems that it cached the results and then when the non-updated code tried to access the same resources it was unable to hit the endpoint.

I have deleted the lsid cache and that seems to have solved many of the problems we all experienced the past few days.

Sorry about that!  It took a while to track down that arcane problem...

Mark

--
Mark Wilkinson
...on the road!


-----Original Message-----
From: "Edward Kawas" <edward.kawas at gmail.com>
Date: Mon, 26 Nov 2007 15:34:15 
To:"'Arnaud Kerhornou'" <arnaud at ebi.ac.uk>,       "'Core developer announcements'" <moby-dev at lists.open-bio.org>,       "'Core developer announcements'" <moby-dev at biomoby.org>
Subject: Re: [MOBY-dev] Parse_moby_data processor in taverna fails

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)



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