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kozo2/gist:a346cd43710d9ef0ab6c

Created May 21, 2014 15:15
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from BioPAX Level3 to SBGN (after removing some tags)
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gistfile1.txt
~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level3.owl l3.sbgn
5363 [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
5364 [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
5364 [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
5364 [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
5364 [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
5365 [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
5365 [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
5365 [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
5922 [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)
SbgnPD Layout is running now...
complexes cleared.
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