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When running using this method: SBMLReader.read(FILE) to read the file Simulation_Environment.xml in the attached Zip file, with either 1.6.0-SNAPSHOT or 1.6.1, we get the exception below. However, there was no error for an earlier version of 1.6.0-SNAPSHOT.
Reading: /Users/myers/Downloads/Simulation_Environment/Simulation_Environment.xml
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 0
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
at java.base/java.util.Objects.checkIndex(Objects.java:372)
at java.base/java.util.ArrayList.get(ArrayList.java:459)
at org.sbml.jsbml.util.compilers.UnitsCompiler.lambda(UnitsCompiler.java:905)
at org.sbml.jsbml.ASTNode.compile(ASTNode.java:2225)
at org.sbml.jsbml.ASTNode.deriveUnit(ASTNode.java:2356)
at org.sbml.jsbml.ASTNode.astNodeToTree(ASTNode.java:4601)
at org.sbml.jsbml.ASTNode.addChild(ASTNode.java:1825)
at org.sbml.jsbml.xml.parsers.MathMLStaxParser.processStartElement(MathMLStaxParser.java:568)
at org.sbml.jsbml.xml.stax.SBMLReader.processStartElement(SBMLReader.java:1004)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromXMLEventReader(SBMLReader.java:767)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromStream(SBMLReader.java:592)
at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:306)
at org.sbml.jsbml.SBMLReader.readSBML(SBMLReader.java:116)
at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:105)
at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:92)
at edu.utah.ece.async.ibiosim.analysis.Analysis.runSEDML(Analysis.java:416)
at edu.utah.ece.async.ibiosim.analysis.Analysis.performAnalysis(Analysis.java:256)
at edu.utah.ece.async.ibiosim.analysis.Analysis.main(Analysis.java:231)
When running using this method: SBMLReader.read(FILE) to read the file Simulation_Environment.xml in the attached Zip file, with either 1.6.0-SNAPSHOT or 1.6.1, we get the exception below. However, there was no error for an earlier version of 1.6.0-SNAPSHOT.
Reading: /Users/myers/Downloads/Simulation_Environment/Simulation_Environment.xml
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 0
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
at java.base/java.util.Objects.checkIndex(Objects.java:372)
at java.base/java.util.ArrayList.get(ArrayList.java:459)
at org.sbml.jsbml.util.compilers.UnitsCompiler.lambda(UnitsCompiler.java:905)
at org.sbml.jsbml.ASTNode.compile(ASTNode.java:2225)
at org.sbml.jsbml.ASTNode.deriveUnit(ASTNode.java:2356)
at org.sbml.jsbml.ASTNode.astNodeToTree(ASTNode.java:4601)
at org.sbml.jsbml.ASTNode.addChild(ASTNode.java:1825)
at org.sbml.jsbml.xml.parsers.MathMLStaxParser.processStartElement(MathMLStaxParser.java:568)
at org.sbml.jsbml.xml.stax.SBMLReader.processStartElement(SBMLReader.java:1004)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromXMLEventReader(SBMLReader.java:767)
at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromStream(SBMLReader.java:592)
at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:306)
at org.sbml.jsbml.SBMLReader.readSBML(SBMLReader.java:116)
at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:105)
at org.sbml.jsbml.SBMLReader.read(SBMLReader.java:92)
at edu.utah.ece.async.ibiosim.analysis.Analysis.runSEDML(Analysis.java:416)
at edu.utah.ece.async.ibiosim.analysis.Analysis.performAnalysis(Analysis.java:256)
at edu.utah.ece.async.ibiosim.analysis.Analysis.main(Analysis.java:231)
Simulation_Environment.zip
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