Program: 12687
Project: 12687
Buggy source:
ComponentDefinition copy(String URIprefix,String displayId,String version){
  ComponentDefinition cloned=this.deepCopy();
  cloned.setWasDerivedFrom(this.getIdentity());
  cloned.setPersistentIdentity(createCompliantURI(URIprefix,displayId,"String_Node_Str"));
  cloned.setDisplayId(displayId);
  cloned.setVersion(version);
  URI newIdentity=createCompliantURI(URIprefix,displayId,version);
  cloned.setIdentity(newIdentity);
  int count=0;
  for (  Component component : cloned.getComponents()) {
    cloned.removeChildSafely(component,components);
    if (!component.isSetDisplayId())     component.setDisplayId("String_Node_Str" + ++count);
    component.updateCompliantURI(cloned.getPersistentIdentity().toString(),component.getDisplayId(),version);
    cloned.addComponent(component);
  }
  count=0;
  for (  SequenceConstraint sequenceConstraint : cloned.getSequenceConstraints()) {
    if (!sequenceConstraint.isSetDisplayId())     sequenceConstraint.setDisplayId("String_Node_Str" + ++count);
    sequenceConstraint.updateCompliantURI(cloned.getPersistentIdentity().toString(),sequenceConstraint.getDisplayId(),version);
  }
  count=0;
  for (  SequenceAnnotation sequenceAnnotation : cloned.getSequenceAnnotations()) {
    if (!sequenceAnnotation.isSetDisplayId())     sequenceAnnotation.setDisplayId("String_Node_Str" + ++count);
    sequenceAnnotation.updateCompliantURI(cloned.getPersistentIdentity().toString(),sequenceAnnotation.getDisplayId(),version);
  }
  return cloned;
}

Fixed version (ground truth):
ComponentDefinition copy(String URIprefix,String displayId,String version){
  ComponentDefinition cloned=this.deepCopy();
  cloned.setWasDerivedFrom(this.getIdentity());
  cloned.setPersistentIdentity(createCompliantURI(URIprefix,displayId,"String_Node_Str"));
  cloned.setDisplayId(displayId);
  cloned.setVersion(version);
  URI newIdentity=createCompliantURI(URIprefix,displayId,version);
  cloned.setIdentity(newIdentity);
  int count=0;
  for (  Component component : cloned.getComponents()) {
    if (!component.isSetDisplayId())     component.setDisplayId("String_Node_Str" + ++count);
    component.updateCompliantURI(cloned.getPersistentIdentity().toString(),component.getDisplayId(),version);
    cloned.removeChildSafely(component,cloned.components);
    cloned.addComponent(component);
  }
  count=0;
  for (  SequenceConstraint sequenceConstraint : cloned.getSequenceConstraints()) {
    if (!sequenceConstraint.isSetDisplayId())     sequenceConstraint.setDisplayId("String_Node_Str" + ++count);
    sequenceConstraint.updateCompliantURI(cloned.getPersistentIdentity().toString(),sequenceConstraint.getDisplayId(),version);
    cloned.removeChildSafely(sequenceConstraint,cloned.sequenceConstraints);
    cloned.addSequenceConstraint(sequenceConstraint);
  }
  count=0;
  for (  SequenceAnnotation sequenceAnnotation : cloned.getSequenceAnnotations()) {
    if (!sequenceAnnotation.isSetDisplayId())     sequenceAnnotation.setDisplayId("String_Node_Str" + ++count);
    sequenceAnnotation.updateCompliantURI(cloned.getPersistentIdentity().toString(),sequenceAnnotation.getDisplayId(),version);
    cloned.removeChildSafely(sequenceAnnotation,cloned.sequenceAnnotations);
    cloned.addSequenceAnnotation(sequenceAnnotation);
  }
  return cloned;
}