Unable to generate models automatically

[Hatem-synbio]

java.lang.NoClassDefFoundError: Could not initialize class org.apache.jena.query.ARQ
at org.apache.jena.sparql.engine.http.QueryEngineHTTP.(QueryEngineHTTP.java:129)
at org.apache.jena.sparql.engine.http.QueryEngineHTTP.(QueryEngineHTTP.java:121)
at org.apache.jena.sparql.engine.http.QueryEngineHTTP.(QueryEngineHTTP.java:113)
at org.virtualparts.data.TripleStoreHandler.executeSparql(TripleStoreHandler.java:34)
at org.virtualparts.data.SBOLStackHandler.getInteractions(SBOLStackHandler.java:62)
at org.virtualparts.data2.SBOLInteractionAdder_GeneCentric.addInteractions(SBOLInteractionAdder_GeneCentric.java:203)
at org.virtualparts.data2.SBOLInteractionAdder_GeneCentric.getInteractions(SBOLInteractionAdder_GeneCentric.java:190)
at org.virtualparts.data2.SBOLInteractionAdder_GeneCentric.addInteractions(SBOLInteractionAdder_GeneCentric.java:83)
at edu.utah.ece.async.ibiosim.conversion.VPRModelGenerator.generateModel(VPRModelGenerator.java:89)
at edu.utah.ece.async.ibiosim.gui.Gui.runVPRGenerator(Gui.java:6064)
at edu.utah.ece.async.ibiosim.gui.Gui.openSBOLOptions(Gui.java:6020)
at edu.utah.ece.async.ibiosim.gui.Gui.executeMouseClickEvent(Gui.java:7362)
at edu.utah.ece.async.ibiosim.gui.Gui.mouseClicked(Gui.java:8202)
at java.desktop/java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:278)
at java.desktop/java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:277)
at java.desktop/java.awt.Component.processMouseEvent(Component.java:6624)
at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3404)
at java.desktop/java.awt.Component.processEvent(Component.java:6386)
at java.desktop/java.awt.Container.processEvent(Container.java:2266)
at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4584)
at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.NoClassDefFoundError: org/apache/xerces/util/XMLChar [in thread "AWT-EventQueue-0"]
at org.apache.jena.rdf.model.impl.Util.notNameChar(Util.java:116)
at org.apache.jena.rdf.model.impl.Util.splitNamespaceXML(Util.java:74)
at org.apache.jena.graph.Node_URI.getLocalName(Node_URI.java:80)
at org.apache.jena.rdf.model.impl.ResourceImpl.getLocalName(ResourceImpl.java:152)
at org.apache.jena.rdf.model.impl.PropertyImpl.checkLocalName(PropertyImpl.java:64)
at org.apache.jena.rdf.model.impl.PropertyImpl.(PropertyImpl.java:72)
at org.apache.jena.rdf.model.ResourceFactory$Impl.createProperty(ResourceFactory.java:301)
at org.apache.jena.rdf.model.ResourceFactory.createProperty(ResourceFactory.java:156)
at org.apache.jena.vocabulary.RDF.property(RDF.java:50)
at org.apache.jena.vocabulary.RDF.(RDF.java:63)
at org.apache.jena.sparql.ARQConstants.(ARQConstants.java:38)
at org.apache.jena.query.ARQ.(ARQ.java:70)
... 45 more

[cjmyers]

Can you provide more detail about what you were doing when you experienced this error? Which SBH were you doing model generation with?

[Hatem-synbio]

Definitely, I was debugging Kenzo's toggle switch model. But I remember I had this problem while creating my TS model before. We had this problem while following the iBioSim tutorial on page 94 for the automatic model generation part. Here is a screenshot of the step:

and here is a screenshot of the SBH selection:

Here is also a screenshot of the exception error:

If you need more information, I can share with you the COMBINE archive on Slack.

[cjmyers]

Yes, send me the OMEX file on slack

[Hatem-synbio]

Done

[cjmyers]

I'm pretty sure the issue has to do with trying to create a model using iGEM parts. iGEM parts do not have interaction information, so it is impossible to generate a model. Granted, there should be a better error than an exception.

To actually test this better, should use the Cello library.

[Hatem-synbio]

Sure thing