[MOBY-dev] BioMOBY errors in Taverna 1.6+

[Edward Kawas]

Hi Pieter,

I will look into it. Something must have happened to the dependencies for
the plugin during the release of the latest version of taverna. Hopefully
its minor!

Eddie 

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Pieter Neerincx
> Sent: Wednesday, September 05, 2007 9:29 AM
> To: Core developer announcements
> Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
> 
> Hi Eddie,
> 
> I just tried Taverna 1.6.0 and 1.6.1 and the processors to 
> decompose complex BioMOBY objects are failing on me :(. Below 
> is the output of a service that produces a generic Object 
> object. All I tried to do was decompose the Object to get the 
> value of the id attribute... It works beautifully in Taverna 
> 1.5.2. Do I have to do something different in 1.6+ or is this a bug?
> 
> Cheers,
> 
> Pi
> ERROR 2007-09-05 17:41:16,696 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-106" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:16,708 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-104" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:19,020 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-116" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          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.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> 
> 
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR) Laboratory of 
> Bioinformatics Transitorium (building 312) room 1034
> 
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
> 
> phone:  0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
> 
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