has only substance units is parsed and exported proeprly

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

@@ -30,6 +30,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     if (element.getInitialAmount() != null) {
       result.setInitialAmount(element.getInitialAmount());
     }
+    if (element.hasOnlySubstanceUnits() != null) {
+      result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
+    }
     return result;
   }
 

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

@@ -37,6 +37,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
       if (!Double.isNaN(species.getInitialAmount())) {
         result.setInitialAmount(species.getInitialAmount());
       }
+      if (species.isSetHasOnlySubstanceUnits()) {
+        result.setOnlySubstanceUnits(species.hasOnlySubstanceUnits());
+      }
       assignBioEntityData(species, result);
       if (layout == null) {
         assignCompartment(result, species.getCompartment());

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java

@@ -152,4 +152,10 @@ public class SbmlSpeciesParserTest {
     Species element = model.getElementByElementId("s1");
     assertEquals((Double)1.0, element.getInitialAmount());
   }
+  @Test
+  public void testParseHasOnlySubstanceUnits() throws Exception {
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/has_only_substance_units.xml"));
+    Species element = model.getElementByElementId("s1");
+    assertTrue(element.hasOnlySubstanceUnits());
+  }
 }

converter-sbml/testFiles/small/has_only_substance_units.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="TestGEN">
+    <annotation/>
+    <listOfCompartments>
+      <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#">
+              <bqbiol:isVersionOf>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+                </rdf:Bag>
+              </bqbiol:isVersionOf>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="cell" hasOnlySubstanceUnits="true" id="s1" name="nm1" sboTerm="SBO:0000247" initialAmount="1">
+        <annotation/>
+      </species>
+    </listOfSpecies>
+  </model>
+</sbml>
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