[MOBY-dev] BioMOBY errors in Taverna 1.6+
Pieter Neerincx
Pieter.Neerincx at wur.nl
Wed Sep 5 16:29:03 UTC 2007
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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:576)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:517)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:436)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.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.ProcessorTask.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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