Program: 12526
Project: 12526
Buggy source:
/** 
 * Top level types
 * @param args 
 * @throws SBOLValidationException 
 * @throws SBOLConversionException 
 * @throws IOException 
 * @throws CoreIoException 
 * @throws XMLStreamException 
 */
public static void main(String[] args) throws SBOLValidationException, SBOLConversionException, IOException {
  SequenceOntology seqOn=new SequenceOntology();
  System.out.println(seqOn.isDescendantOf(SequenceOntology.TERMINATOR,URI.create("String_Node_Str")));
  for (  URI child : seqOn.getDescendantURIsOf(SequenceOntology.TERMINATOR)) {
    System.out.println(child.toString());
  }
  SBOLDocument document=new SBOLDocument();
  document.setDefaultURIprefix("String_Node_Str");
  ComponentDefinition cd=document.createComponentDefinition("String_Node_Str",ComponentDefinition.DNA);
  document.createComponentDefinition("String_Node_Str",ComponentDefinition.DNA);
  Component comp=cd.createComponent("String_Node_Str",AccessType.PRIVATE,"String_Node_Str");
  comp.addRole(SequenceOntology.PROMOTER);
  comp.setRoleIntegration(RoleIntegrationType.MERGEROLES);
  SequenceAnnotation sa=cd.createSequenceAnnotation("String_Node_Str","String_Node_Str");
  sa.addRole(SequenceOntology.PROMOTER);
  sa.setRoleIntegration(RoleIntegrationType.OVERRIDEROLES);
  SBOLDocument actual=SBOLTestUtils.writeAndRead(document,true);
  actual.write(System.out);
  Sequence seq=document.createSequence("String_Node_Str","String_Node_Str",org.sbolstandard.core2.Sequence.IUPAC_DNA);
  document.addNamespace(URI.create("String_Node_Str"),"String_Node_Str");
  Annotation an=new Annotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  Annotation an2=new Annotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  List<Annotation> annos=new ArrayList<Annotation>();
  annos.add(an);
  annos.add(an2);
  seq.createAnnotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),new QName("String_Node_Str","String_Node_Str","String_Node_Str"),URI.create("String_Node_Str"),annos);
  get_myParts(sbolDocument);
  sbolDocument.getComponentDefinition("String_Node_Str","String_Node_Str");
  SBOLValidate.validateSBOL(sbolDocument,true,true,true);
  if (SBOLValidate.getNumErrors() > 0) {
    for (    String error : SBOLValidate.getErrors()) {
      System.out.println(error);
    }
  }
  SBOLWriter.write(sbolDocument,(System.out),SBOLDocument.RDFV1);
}

Fixed version (ground truth):
/** 
 * Top level types
 * @param args 
 * @throws SBOLValidationException 
 * @throws SBOLConversionException 
 * @throws IOException 
 * @throws CoreIoException 
 * @throws XMLStreamException 
 */
public static void main(String[] args) throws SBOLValidationException, SBOLConversionException, IOException {
  SequenceOntology seqOn=new SequenceOntology();
  System.out.println(seqOn.isDescendantOf(SequenceOntology.TERMINATOR,URI.create("String_Node_Str")));
  for (  URI child : seqOn.getDescendantURIsOf(SequenceOntology.TERMINATOR)) {
    System.out.println(child.toString());
  }
  SBOLDocument document=new SBOLDocument();
  document.setDefaultURIprefix("String_Node_Str");
  ComponentDefinition cd=document.createComponentDefinition("String_Node_Str",ComponentDefinition.DNA);
  document.createComponentDefinition("String_Node_Str",ComponentDefinition.DNA);
  Component comp=cd.createComponent("String_Node_Str",AccessType.PRIVATE,"String_Node_Str");
  comp.setDefinition(cd.getIdentity());
  comp.addRole(SequenceOntology.PROMOTER);
  comp.setRoleIntegration(RoleIntegrationType.MERGEROLES);
  SequenceAnnotation sa=cd.createSequenceAnnotation("String_Node_Str","String_Node_Str");
  sa.addRole(SequenceOntology.PROMOTER);
  sa.setRoleIntegration(RoleIntegrationType.OVERRIDEROLES);
  SBOLDocument actual=SBOLTestUtils.writeAndRead(document,true);
  actual.write(System.out);
  Sequence seq=document.createSequence("String_Node_Str","String_Node_Str",org.sbolstandard.core2.Sequence.IUPAC_DNA);
  document.addNamespace(URI.create("String_Node_Str"),"String_Node_Str");
  Annotation an=new Annotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  Annotation an2=new Annotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),"String_Node_Str");
  List<Annotation> annos=new ArrayList<Annotation>();
  annos.add(an);
  annos.add(an2);
  seq.createAnnotation(new QName("String_Node_Str","String_Node_Str","String_Node_Str"),new QName("String_Node_Str","String_Node_Str","String_Node_Str"),URI.create("String_Node_Str"),annos);
  get_myParts(sbolDocument);
  sbolDocument.getComponentDefinition("String_Node_Str","String_Node_Str");
  SBOLValidate.validateSBOL(sbolDocument,true,true,true);
  if (SBOLValidate.getNumErrors() > 0) {
    for (    String error : SBOLValidate.getErrors()) {
      System.out.println(error);
    }
  }
  SBOLWriter.write(sbolDocument,(System.out),SBOLDocument.RDFV1);
}