export contains list of species type for multi package

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java

@@ -16,6 +16,8 @@ import org.sbml.jsbml.SBMLWriter;
 import org.sbml.jsbml.ext.layout.Dimensions;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.sbml.jsbml.ext.multi.MultiSpeciesType;
 import org.sbml.jsbml.ext.render.GlobalRenderInformation;
 import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
 
@@ -26,7 +28,9 @@ import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
 import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class SbmlExporter {
 
@@ -79,6 +83,10 @@ public class SbmlExporter {
       layout = createSbmlLayout(model, result);
     }
 
+    if (usedExtensions.contains(SbmlExtension.MULTI)) {
+      createSbmlMultiPlugin(model, result);
+    }
+
     SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model, usedExtensions);
     SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
         usedExtensions,
@@ -132,6 +140,20 @@ public class SbmlExporter {
     return layout;
   }
 
+  public MultiModelPlugin createSbmlMultiPlugin(lcsb.mapviewer.model.map.model.Model model, Model result) {
+    MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
+    result.addExtension("multi", multiPlugin);
+    for (Class<? extends Element> clazz : new ElementUtils().getAvailableElementSubclasses()) {
+      if (Species.class.isAssignableFrom(clazz)) {
+        MultiSpeciesType speciesType = new MultiSpeciesType();
+        speciesType.setName(clazz.getSimpleName());
+        speciesType.setId("minerva_species_type_" + clazz.getSimpleName());
+        multiPlugin.getListOfSpeciesTypes().add(speciesType);
+      }
+    }
+    return multiPlugin;
+  }
+
   /**
    * Creates SBML render plugin for SBML model.
    * 

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

@@ -18,6 +18,7 @@ import java.util.Set;
 import org.apache.log4j.Logger;
 import org.junit.Test;
 import org.reflections.Reflections;
+import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.ConverterParams;
@@ -362,10 +363,10 @@ public class SbmlExporterTest {
     SbmlExporter exporter = new SbmlExporter();
     exporter.removeSbmlExtensions(Arrays.asList(SbmlExtension.values()));
     exporter.addSbmlExtension(SbmlExtension.LAYOUT);
-    
+
     Model model = createModelWithReaction();
     String xml = exporter.toXml(model);
-    
+
     assertTrue(xml.contains("layout:listOfLayouts"));
   }
 
@@ -373,10 +374,10 @@ public class SbmlExporterTest {
   public void testExportWithoutLayoutExtension() throws Exception {
     SbmlExporter exporter = new SbmlExporter();
     exporter.removeSbmlExtensions(Arrays.asList(SbmlExtension.values()));
-    
+
     Model model = createModelWithReaction();
     String xml = exporter.toXml(model);
-    
+
     assertFalse(xml.contains("layout:listOfLayouts"));
   }
 
@@ -386,10 +387,10 @@ public class SbmlExporterTest {
     exporter.removeSbmlExtensions(Arrays.asList(SbmlExtension.values()));
     exporter.addSbmlExtension(SbmlExtension.LAYOUT);
     exporter.addSbmlExtension(SbmlExtension.RENDER);
-    
+
     Model model = createModelWithReaction();
     String xml = exporter.toXml(model);
-    
+
     assertTrue(xml.contains("render:listOfRenderInformation"));
   }
 
@@ -398,11 +399,24 @@ public class SbmlExporterTest {
     SbmlExporter exporter = new SbmlExporter();
     exporter.removeSbmlExtensions(Arrays.asList(SbmlExtension.values()));
     exporter.addSbmlExtension(SbmlExtension.LAYOUT);
-    
+
     Model model = createModelWithReaction();
     String xml = exporter.toXml(model);
-    
+
     assertFalse(xml.contains("render:listOfRenderInformation"));
   }
 
+  @Test
+  public void testExportWithoutMultiExtensionSupportSpeciesTypes() throws Exception {
+    SbmlExporter exporter = new SbmlExporter();
+    exporter.removeSbmlExtensions(Arrays.asList(SbmlExtension.values()));
+    exporter.addSbmlExtension(SbmlExtension.MULTI);
+
+    org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(createModelWithReaction()).getModel();
+    MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
+    assertNotNull("Multi plugin is not present in sbml model", multiPlugin);
+
+    assertTrue("Species types are not exported", multiPlugin.getListOfSpeciesTypes().size() > 0);
+  }
+
 }