Program: 12561
Project: 12561
Buggy source:
public static void main(String[] args) throws XMLStreamException, FactoryConfigurationError, CoreIoException, IOException, SBOLValidationException {
  String prURI="String_Node_Str";
  String prPrefix="String_Node_Str";
  String myersLabURI="String_Node_Str";
  String myersLabPrefix="String_Node_Str";
  SBOLDocument document=new SBOLDocument();
  document.setDefaultURIprefix(prURI);
  document.setTypesInURIs(true);
  document.setComplete(true);
  document.setCreateDefaults(true);
  document.addNamespace(URI.create(prURI),prPrefix);
  document.addNamespace(URI.create(myersLabURI),myersLabPrefix);
  HashSet<URI> types=new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA,URI.create("String_Node_Str")));
  ComponentDefinition TetR_promoter=document.createComponentDefinition("String_Node_Str",types);
  ComponentDefinition LacI_repressor=document.createComponentDefinition("String_Node_Str",types);
  ComponentDefinition pIKELeftCassette=document.createComponentDefinition("String_Node_Str",types);
  Sequence seq_187=document.createSequence("String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  String element2="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  Sequence seq_153=document.createSequence("String_Node_Str",element2,Sequence.IUPAC_DNA);
  TetR_promoter.setName("String_Node_Str");
  LacI_repressor.setName("String_Node_Str");
  TetR_promoter.setDescription("String_Node_Str");
  LacI_repressor.setDescription("String_Node_Str");
  if (TetR_promoter.isSetName()) {
    TetR_promoter.unsetName();
  }
  TetR_promoter.setName("String_Node_Str");
  TetR_promoter.addRole(SequenceOntology.PROMOTER);
  LacI_repressor.addRole(SequenceOntology.CDS);
  URI TetR_promoter_role2=URI.create("String_Node_Str");
  TetR_promoter.addRole(TetR_promoter_role2);
  if (TetR_promoter.containsRole(TetR_promoter_role2)) {
    TetR_promoter.removeRole(TetR_promoter_role2);
  }
  TetR_promoter.clearRoles();
  if (!TetR_promoter.getRoles().isEmpty()) {
    System.out.println("String_Node_Str");
  }
  TetR_promoter.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
  TetR_promoter.addSequence(seq_187);
  LacI_repressor.addSequence(seq_153);
  pIKELeftCassette.addSequence(seq_187);
  pIKELeftCassette.clearSequences();
  TetR_promoter.createAnnotation(new QName(prURI,"String_Node_Str",prPrefix),URI.create("String_Node_Str"));
  GenericTopLevel datasheet=document.createGenericTopLevel("String_Node_Str","String_Node_Str",new QName(myersLabURI,"String_Node_Str",myersLabPrefix));
  datasheet.setName("String_Node_Str");
  datasheet.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),URI.create(myersLabURI + "String_Node_Str"));
  datasheet.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),"String_Node_Str");
  TetR_promoter.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),datasheet.getIdentity());
  pIKELeftCassette.createSequenceConstraint("String_Node_Str",RestrictionType.PRECEDES,TetR_promoter.getDisplayId(),LacI_repressor.getDisplayId());
  if (pIKELeftCassette.getComponent("String_Node_Str") == null) {
    System.out.println("String_Node_Str");
  }
  if (pIKELeftCassette.getComponent("String_Node_Str") == null) {
    System.out.println("String_Node_Str");
  }
  ComponentDefinition TetR_promoter_copy=(ComponentDefinition)document.createCopy(TetR_promoter,"String_Node_Str");
  Sequence seq=document.createSequence("String_Node_Str","String_Node_Str" + "String_Node_Str" + "String_Node_Str",Sequence.IUPAC_DNA);
  TetR_promoter_copy.addSequence(seq);
  SBOLWriter.write(document,"String_Node_Str");
  writeThenRead(document);
}

Fixed version (ground truth):
public static void main(String[] args) throws XMLStreamException, FactoryConfigurationError, CoreIoException, IOException, SBOLValidationException, SBOLConversionException {
  String prURI="String_Node_Str";
  String prPrefix="String_Node_Str";
  String myersLabURI="String_Node_Str";
  String myersLabPrefix="String_Node_Str";
  SBOLDocument document=new SBOLDocument();
  document.setDefaultURIprefix(prURI);
  document.setTypesInURIs(true);
  document.setComplete(true);
  document.setCreateDefaults(true);
  document.addNamespace(URI.create(prURI),prPrefix);
  document.addNamespace(URI.create(myersLabURI),myersLabPrefix);
  HashSet<URI> types=new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA,URI.create("String_Node_Str")));
  ComponentDefinition TetR_promoter=document.createComponentDefinition("String_Node_Str",types);
  ComponentDefinition LacI_repressor=document.createComponentDefinition("String_Node_Str",types);
  ComponentDefinition pIKELeftCassette=document.createComponentDefinition("String_Node_Str",types);
  Sequence seq_187=document.createSequence("String_Node_Str","String_Node_Str",Sequence.IUPAC_DNA);
  String element2="String_Node_Str" + "String_Node_Str" + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str";
  Sequence seq_153=document.createSequence("String_Node_Str",element2,Sequence.IUPAC_DNA);
  TetR_promoter.setName("String_Node_Str");
  LacI_repressor.setName("String_Node_Str");
  TetR_promoter.setDescription("String_Node_Str");
  LacI_repressor.setDescription("String_Node_Str");
  if (TetR_promoter.isSetName()) {
    TetR_promoter.unsetName();
  }
  TetR_promoter.setName("String_Node_Str");
  TetR_promoter.addRole(SequenceOntology.PROMOTER);
  LacI_repressor.addRole(SequenceOntology.CDS);
  URI TetR_promoter_role2=URI.create("String_Node_Str");
  TetR_promoter.addRole(TetR_promoter_role2);
  if (TetR_promoter.containsRole(TetR_promoter_role2)) {
    TetR_promoter.removeRole(TetR_promoter_role2);
  }
  TetR_promoter.clearRoles();
  if (!TetR_promoter.getRoles().isEmpty()) {
    System.out.println("String_Node_Str");
  }
  TetR_promoter.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
  TetR_promoter.addSequence(seq_187);
  LacI_repressor.addSequence(seq_153);
  pIKELeftCassette.addSequence(seq_187);
  pIKELeftCassette.clearSequences();
  TetR_promoter.createAnnotation(new QName(prURI,"String_Node_Str",prPrefix),URI.create("String_Node_Str"));
  GenericTopLevel datasheet=document.createGenericTopLevel("String_Node_Str","String_Node_Str",new QName(myersLabURI,"String_Node_Str",myersLabPrefix));
  datasheet.setName("String_Node_Str");
  datasheet.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),URI.create(myersLabURI + "String_Node_Str"));
  datasheet.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),"String_Node_Str");
  TetR_promoter.createAnnotation(new QName(myersLabURI,"String_Node_Str",myersLabPrefix),datasheet.getIdentity());
  pIKELeftCassette.createSequenceConstraint("String_Node_Str",RestrictionType.PRECEDES,TetR_promoter.getDisplayId(),LacI_repressor.getDisplayId());
  if (pIKELeftCassette.getComponent("String_Node_Str") == null) {
    System.out.println("String_Node_Str");
  }
  if (pIKELeftCassette.getComponent("String_Node_Str") == null) {
    System.out.println("String_Node_Str");
  }
  ComponentDefinition TetR_promoter_copy=(ComponentDefinition)document.createCopy(TetR_promoter,"String_Node_Str");
  Sequence seq=document.createSequence("String_Node_Str","String_Node_Str" + "String_Node_Str" + "String_Node_Str",Sequence.IUPAC_DNA);
  TetR_promoter_copy.addSequence(seq);
  SBOLWriter.write(document,"String_Node_Str");
  writeThenRead(document);
}