Comments (2)
@MafGal Yes, the file is valid, but there seem to some issues with the annotations which make the JSBML parser fail. The underlying error is
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 575; The element type "link" must be terminated by the matching end-tag "</link>".
This comes from some parts of the annotations:
at org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser.readRDFURIs(SBMLRDFAnnotationParser.java:991)
at org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser.readSBMLRDF(SBMLRDFAnnotationParser.java:490)
at org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser.processAnnotation(SBMLRDFAnnotationParser.java:115)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromXMLEventReader(SBMLReader.java:851)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromStream(SBMLReader.java:592)
at org.sbml.jsbml.xml.stax.SBMLReader.readSBMLFromString(SBMLReader.java:904)
at org.sbml.jsbml.xml.stax.SBMLReader.readSBMLFromString(SBMLReader.java:918)
at org.sbml.jsbml.SBMLReader.readSBMLFromString(SBMLReader.java:264)
at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:140)
at org.sbml.jsbml.JSBML.readSBMLFromString(JSBML.java:425)
at org.cy3sbml.SBMLReaderTask.run(SBMLReaderTask.java:273)
I will test this with the latest version of JSBML and open an issue on the JSBML page for this.
Sorry for the inconvenience.
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Thanks a lot Matthias! @matthiaskoenig
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