Program: 12435
Project: 12435
Buggy source:
private void fixDocumentURIPrefix() throws SBOLValidationException {
  String documentURIPrefixAll=extractDocumentURIPrefix();
  if (documentURIPrefixAll.length() >= 9) {
    setDefaultURIprefix(documentURIPrefixAll);
  }
  String documentURIPrefix=documentURIPrefixAll;
  for (  TopLevel topLevel : getTopLevels()) {
    if (documentURIPrefixAll.length() < 9) {
      documentURIPrefix=URIcompliance.extractURIprefix(topLevel.getIdentity());
      String documentURIPrefix2=URIcompliance.extractURIprefix(URI.create(URIcompliance.extractSimpleNamespace(topLevel.getIdentity())));
      if (documentURIPrefix2 != null) {
        documentURIPrefix=documentURIPrefix2;
      }
    }
    if (!topLevel.getIdentity().equals(URIcompliance.createCompliantURI(documentURIPrefix,topLevel.getDisplayId(),topLevel.getVersion()))) {
      String newDisplayId=topLevel.getIdentity().toString().replaceAll(documentURIPrefix,"String_Node_Str");
      String newVersion="String_Node_Str";
      if (topLevel.isSetVersion()) {
        newDisplayId=newDisplayId.replace("String_Node_Str" + topLevel.getVersion(),"String_Node_Str");
        newVersion=topLevel.getVersion();
      }
      newDisplayId=URIcompliance.fixDisplayId(newDisplayId);
      while (getTopLevel(URIcompliance.createCompliantURI(documentURIPrefix,newDisplayId,newVersion)) != null) {
        newDisplayId=newDisplayId.replaceAll("String_Node_Str","String_Node_Str");
      }
      TopLevel newTopLevel=this.createCopy(topLevel,newDisplayId,newVersion);
      removeTopLevel(topLevel);
      updateReferences(topLevel.getIdentity(),newTopLevel.getIdentity());
      updateReferences(topLevel.getPersistentIdentity(),newTopLevel.getPersistentIdentity());
    }
  }
}

Fixed version (ground truth):
private void fixDocumentURIPrefix() throws SBOLValidationException {
  String documentURIPrefixAll=extractDocumentURIPrefix();
  if (documentURIPrefixAll != null && documentURIPrefixAll.length() >= 9) {
    setDefaultURIprefix(documentURIPrefixAll);
  }
  String documentURIPrefix=documentURIPrefixAll;
  for (  TopLevel topLevel : getTopLevels()) {
    if (documentURIPrefixAll.length() < 9) {
      documentURIPrefix=URIcompliance.extractURIprefix(topLevel.getIdentity());
      String simpleNamespace=URIcompliance.extractSimpleNamespace(topLevel.getIdentity());
      if (simpleNamespace != null) {
        String documentURIPrefix2=URIcompliance.extractURIprefix(URI.create(simpleNamespace));
        if (documentURIPrefix2 != null) {
          documentURIPrefix=documentURIPrefix2;
        }
      }
      if (documentURIPrefix == null) {
        documentURIPrefix=this.getDefaultURIprefix();
      }
    }
    if (!topLevel.getIdentity().equals(URIcompliance.createCompliantURI(documentURIPrefix,URIcompliance.findDisplayId(topLevel),topLevel.getVersion()))) {
      String newDisplayId=topLevel.getIdentity().toString().replaceAll(documentURIPrefix,"String_Node_Str");
      String newVersion="String_Node_Str";
      if (topLevel.isSetVersion()) {
        newDisplayId=newDisplayId.replace("String_Node_Str" + topLevel.getVersion(),"String_Node_Str");
        newVersion=topLevel.getVersion();
      }
      newDisplayId=URIcompliance.fixDisplayId(newDisplayId);
      while (getTopLevel(URIcompliance.createCompliantURI(documentURIPrefix,newDisplayId,newVersion)) != null) {
        newDisplayId=newDisplayId.replaceAll("String_Node_Str","String_Node_Str");
      }
      TopLevel newTopLevel=this.createCopy(topLevel,newDisplayId,newVersion);
      removeTopLevel(topLevel);
      updateReferences(topLevel.getIdentity(),newTopLevel.getIdentity());
      updateReferences(topLevel.getPersistentIdentity(),newTopLevel.getPersistentIdentity());
    }
  }
}