unit test to check import export of structural state

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

@@ -13,12 +13,15 @@ import java.io.File;
 import java.lang.reflect.Modifier;
 import java.nio.file.Files;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Set;
 
 import org.apache.log4j.Logger;
 import org.junit.Test;
 import org.reflections.Reflections;
+import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.sbml.jsbml.ext.multi.MultiSpeciesType;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.ConverterParams;
@@ -37,9 +40,13 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
 
 public class SbmlExporterTest {
   Logger logger = Logger.getLogger(SbmlExporterTest.class);
@@ -419,4 +426,59 @@ public class SbmlExporterTest {
     assertTrue("Species types are not exported", multiPlugin.getListOfSpeciesTypes().size() > 0);
   }
 
+  @Test
+  public void testMultiExtensionTypeWithStructuralState() throws Exception {
+    SbmlExporter exporter = new SbmlExporter();
+    SBMLDocument doc = new SBMLDocument(3, 2);
+    org.sbml.jsbml.Model result = doc.createModel("id");
+    MultiModelPlugin multiPlugin = exporter.createSbmlMultiPlugin(result);
+
+    Set<Class<?>> typesWithStructuralStates = new HashSet<>();
+    typesWithStructuralStates.addAll(Arrays.asList(new Class<?>[] { GenericProtein.class, TruncatedProtein.class,
+        Complex.class, IonChannelProtein.class, ReceptorProtein.class }));
+
+    for (Class<?> clazz : typesWithStructuralStates) {
+      MultiSpeciesType speciesType = multiPlugin
+          .getSpeciesType("minerva_species_type_" + clazz.getSimpleName());
+      assertTrue(clazz.getSimpleName() + " doesn't have any features, but at least structuralState expected",
+          speciesType.getListOfSpeciesFeatureTypes().size() > 0);
+
+    }
+
+  }
+
+  @Test
+  public void testMultiExtensionSBOTermsForTypes() throws Exception {
+    SbmlExporter exporter = new SbmlExporter();
+    SBMLDocument doc = new SBMLDocument(3, 2);
+    org.sbml.jsbml.Model result = doc.createModel("id");
+    MultiModelPlugin multiPlugin = exporter.createSbmlMultiPlugin(result);
+
+    for (MultiSpeciesType speciesType : multiPlugin.getListOfSpeciesTypes()) {
+      assertNotNull("SBO term not defined for type " + speciesType.getName(), speciesType.getSBOTermID());
+      assertFalse("SBO term not defined for type " + speciesType.getName(), speciesType.getSBOTermID().isEmpty());
+    }
+
+  }
+
+  @Test
+  public void testExportProteinState() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.setIdModel("Test123");
+    model.setName("x");
+    model.setWidth("300");
+    model.setHeight("300");
+    GenericProtein element = new GenericProtein("id");
+    element.setName("test name");
+    element.setX(10);
+    element.setWidth(10);
+    element.setY(10);
+    element.setHeight(10);
+    element.setStructuralState("xxx");
+    model.addElement(element);
+    Model deserializedModel = getModelAfterSerializing(model);
+
+    assertEquals("Structural state not exported/imported properly", 0, comparator.compare(model, deserializedModel));
+  }
+
 }