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kozo2/paxtools-tosbgn-l3

Created May 4, 2014 10:26
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error log for level3
Raw
paxtools-tosbgn-l3
~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level3.owl l3.sbgn
6014 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference107862 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference107862. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference84097 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference84097. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104062 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104062. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104071 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104071. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference78078 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference78078. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference87952 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference87952. null
6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference147872 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference147872. null
6609 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: NIL (element: http://biocyc.org/biopax/biopax-level3SmallMolecule130719 property: entityReference)
6712 [main] ERROR org.biopax.paxtools.io.BioPAXIOHandlerAdapter - Editor is null. This probably means an invalid BioPAX property. Failed to set 3.6.3.-
Exception in thread "main" java.lang.StackOverflowError
at java.util.Arrays.copyOf(Arrays.java:2760)
at java.util.Arrays.copyOf(Arrays.java:2734)
at java.util.ArrayList.toArray(ArrayList.java:275)
at java.util.ArrayList.addAll(ArrayList.java:472)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.createGlyphBasics(L3ToSBGNPDConverter.java:437)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.createComplexMember(L3ToSBGNPDConverter.java:533)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:509)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
at org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter.addComplexAsMember(L3ToSBGNPDConverter.java:516)
@IgorRodchenkov

IgorRodchenkov commented Feb 16, 2016

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Why are you trying to convert the BioPAX specification (biopax-level3.owl OWL ontology) to SBGN? It's not a BioPAX model, it's BioPAX definition itself...
Unless.. your biopax-level3.owl is a data file (with confusing name), and it's incorrect..
I guess, there are cycles in Complex.component property that causes endless loop and StackOverflowError...

Sorry, I just came across this page accidentally

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