serialization bug in java native

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.12"
+version = "0.0.13"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <schaff@uchc.edu>", "Ezequiel Valencia <evalencia@uchc.edu>"]
 repository = "https://github.com/virtualcell/libvcell"

vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java

@@ -35,6 +35,7 @@ public static void sbml_to_vcml(String sbml_content, Path vcmlPath)
 
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         record LoggerMessage(VCLogger.Priority priority, VCLogger.ErrorType errorType, String message) {};
         final ArrayList<LoggerMessage> messages = new ArrayList<>();
@@ -76,6 +77,7 @@ public static void vcml_to_sbml(String vcml_content, String applicationName, Pat
             throws XmlParseException, IOException, XMLStreamException, SbmlException, MappingException, ImageException, GeometryException, ExpressionException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
@@ -115,6 +117,7 @@ public static void vcml_to_sbml(String vcml_content, String applicationName, Pat
     public static void vcml_to_vcml(String vcml_content, Path vcmlPath) throws XmlParseException, IOException, MappingException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);

vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java

@@ -41,6 +41,8 @@ public class SolverUtils {
     public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File parentDir, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException, MathException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
+
         if (vcml_content.substring(0, 300).contains("<sbml xmlns=\"http://www.sbml.org/sbml")) {
             throw new IllegalArgumentException("expecting VCML content, not SBML");
         }
@@ -134,6 +136,8 @@ private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation
     public static void sbmlToFiniteVolumeInput(String sbml_content, File outputDir) throws MappingException, PropertyVetoException, SolverException, ExpressionException, VCLoggerException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
+
         SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger();
         boolean bValidateSBML = true;
         // input stream from sbml_content String