export of position to compartment uses proper names

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java

@@ -8,7 +8,7 @@ public enum BioEntityFeature {
   STRUCTURAL_STATE("Structural state", "", new Class<?>[] { Protein.class, Complex.class },
       "minerva_structural_state_"),
 
-  POSITION_TO_COMPARTMENT("Position to compartment", "undefined", new Class<?>[] { Element.class },
+  POSITION_TO_COMPARTMENT("Position to compartment", MultiPackageNamingUtils.NULL_REPRESENTATION, new Class<?>[] { Element.class },
       "minerva_position_to_compartment_"),
 
   SYNONYM("Synonym", null, new Class<?>[] { Element.class },

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

@@ -266,9 +266,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
 
   private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
-    String value = "undefined";
+    String value = MultiPackageNamingUtils.NULL_REPRESENTATION;
     if (element.getPositionToCompartment() != null) {
-      value = element.getPositionToCompartment().name();
+      value = element.getPositionToCompartment().getStringName();
     }
     assignValueToFeature(element, multiExtension, speciesType, value, BioEntityFeature.POSITION_TO_COMPARTMENT);
   }
@@ -289,17 +289,23 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
 
   private void assignSymbolToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
-    assignValueToFeature(element, multiExtension, speciesType, element.getSymbol(), BioEntityFeature.SYMBOL);
+    if (element.getSymbol() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getSymbol(), BioEntityFeature.SYMBOL);
+    }
   }
 
   private void assignFullNameToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
-    assignValueToFeature(element, multiExtension, speciesType, element.getFullName(), BioEntityFeature.FULL_NAME);
+    if (element.getFullName() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getFullName(), BioEntityFeature.FULL_NAME);
+    }
   }
 
   private void assignFormulaToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
-    assignValueToFeature(element, multiExtension, speciesType, element.getFormula(), BioEntityFeature.FORMULA);
+    if (element.getFormula() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getFormula(), BioEntityFeature.FORMULA);
+    }
   }
 
   private void assignDimerToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -335,8 +341,10 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
 
   private void assignAbbreviationToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
-    assignValueToFeature(element, multiExtension, speciesType, element.getAbbreviation(),
-        BioEntityFeature.ABBREVIATION);
+    if (element.getAbbreviation() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getAbbreviation(),
+          BioEntityFeature.ABBREVIATION);
+    }
   }
 
   private void assignValueToFeature(Species element, MultiSpeciesPlugin multiExtension, MultiSpeciesType speciesType,

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -467,6 +467,18 @@ public class SbmlExporterTest {
         comparator.compare(model, deserializedModel));
   }
 
+  @Test
+  public void testExportOuterSurfacePositionToCompartment() throws Exception {
+    Model model = createEmptyModel();
+    GenericProtein element = createProtein();
+    element.setPositionToCompartment(PositionToCompartment.OUTER_SURFACE);
+    model.addElement(element);
+    Model deserializedModel = getModelAfterSerializing(model);
+
+    assertEquals("Postion to compartment not exported/imported properly", 0,
+        comparator.compare(model, deserializedModel));
+  }
+
   @Test
   public void testMultiExtensionProteinStateInTypes() throws Exception {
     String structuralState = "xxx";