Program: 12717
Project: 12717
Buggy source:
private static Collection parseCollectionV1(SBOLDocument SBOLDoc,IdentifiableDocument<QName> topLevel){
  URI identity=topLevel.getIdentity();
  URI persistentIdentity=null;
  String displayId=null;
  String name=null;
  String description=null;
  Set<URI> members=new HashSet<>();
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol1Terms.Collection.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
      displayId=fixDisplayId(displayId);
      if (setURIPrefix != null) {
        identity=URI.create(setURIPrefix + "String_Node_Str" + TopLevel.COLLECTION+ "String_Node_Str"+ displayId+ "String_Node_Str");
        persistentIdentity=URI.create(setURIPrefix + "String_Node_Str" + TopLevel.COLLECTION+ "String_Node_Str"+ displayId);
      }
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.name)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.description)) {
      description=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.component)) {
      members.add(parseDnaComponentV1(SBOLDoc,(NestedDocument<QName>)namedProperty.getValue()).getIdentity());
    }
 else {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Collection c=SBOLDoc.createCollection(identity);
  if (persistentIdentity != null) {
    c.setPersistentIdentity(persistentIdentity);
    c.setVersion("String_Node_Str");
  }
  if (identity != topLevel.getIdentity())   c.setWasDerivedFrom(topLevel.getIdentity());
  if (displayId != null)   c.setDisplayId(displayId);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (!members.isEmpty())   c.setMembers(members);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  return c;
}

Fixed version (ground truth):
private static Collection parseCollectionV1(SBOLDocument SBOLDoc,IdentifiableDocument<QName> topLevel){
  URI identity=topLevel.getIdentity();
  URI persistentIdentity=null;
  String displayId=null;
  String name=null;
  String description=null;
  Set<URI> members=new HashSet<>();
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol1Terms.Collection.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
      displayId=fixDisplayId(displayId);
      if (URIPrefix != null) {
        identity=createCompliantURI(URIPrefix,TopLevel.COLLECTION,displayId,version,typesInURI);
        persistentIdentity=createCompliantURI(URIPrefix,TopLevel.COLLECTION,displayId,"String_Node_Str",typesInURI);
      }
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.name)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.description)) {
      description=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol1Terms.Collection.component)) {
      members.add(parseDnaComponentV1(SBOLDoc,(NestedDocument<QName>)namedProperty.getValue()).getIdentity());
    }
 else {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Collection c=SBOLDoc.createCollection(identity);
  if (persistentIdentity != null) {
    c.setPersistentIdentity(persistentIdentity);
    c.setVersion(version);
  }
  if (identity != topLevel.getIdentity())   c.setWasDerivedFrom(topLevel.getIdentity());
  if (displayId != null)   c.setDisplayId(displayId);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (!members.isEmpty())   c.setMembers(members);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  return c;
}