Merge branch '577-export-to-sbml-results-in-invalid-sbml-file' into 'master'

Resolve "Export to SBML results in invalid SBML file"

Closes #577

See merge request !508

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

@@ -38,7 +38,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   private Map<String, S> sbmlElementByElementId = new HashMap<>();
   Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
 
-  private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
+  protected Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
 
   private int idCounter = 0;
 
@@ -150,16 +150,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   protected ColorDefinition getColorDefinition(Color color) {
     RenderLayoutPlugin renderPlugin = getRenderPlugin();
 
-    LocalRenderInformation renderInformation = null;
-    for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
-      if (lri.getId().equals("minerva_definitions")) {
-        renderInformation = lri;
-      }
-    }
-    if (renderInformation == null) {
-      renderInformation = new LocalRenderInformation("minerva_definitions");
-      renderPlugin.addLocalRenderInformation(renderInformation);
-    }
+    LocalRenderInformation renderInformation = getRenderInformation(renderPlugin);
 
     for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
       if (cd.getValue().equals(color)) {
@@ -168,11 +159,24 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     }
     ColorDefinition colorDefinition = new ColorDefinition("color_" + colorToString(color), color);
 
-
     renderInformation.addColorDefinition(colorDefinition);
     return colorDefinition;
   }
 
+  protected LocalRenderInformation getRenderInformation(RenderLayoutPlugin renderPlugin) {
+    LocalRenderInformation renderInformation = null;
+    for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+      if (lri.getId().equals("minerva_definitions")) {
+        renderInformation = lri;
+      }
+    }
+    if (renderInformation == null) {
+      renderInformation = new LocalRenderInformation("minerva_definitions");
+      renderPlugin.addLocalRenderInformation(renderInformation);
+    }
+    return renderInformation;
+  }
+
   protected void assignStyleToGlyph(AbstractReferenceGlyph speciesGlyph, LocalStyle style) {
     RenderGraphicalObjectPlugin rgop = new RenderGraphicalObjectPlugin(speciesGlyph);
     rgop.setObjectRole(style.getRoleList().get(0));
@@ -181,12 +185,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   protected LocalStyle createStyle(T element) {
-    LocalRenderInformation renderInformation = new LocalRenderInformation();
+    LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
     LocalStyle style = new LocalStyle();
     style.getRoleList().add("style_" + element.getElementId());
     style.setGroup(new RenderGroup());
     renderInformation.addLocalStyle(style);
-    getRenderPlugin().addLocalRenderInformation(renderInformation);
     return style;
   }
 

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

-package lcsb.mapviewer.converter.model.sbml;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.Layout;
-
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-
-public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
-  Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
-
-  public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
-    super(layout, minervaModel);
-  }
-
-  @Override
-  public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
-    return getSbmlModel().createCompartment("comp_" + (getNextId()));
-  }
-
-  @Override
-  protected List<Compartment> getElementList() {
-    return getMinervaModel().getCompartments();
-  }
-
-  @Override
-  protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
-    return getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
-  }
-
-  @Override
-  protected String getSbmlIdKey(Compartment element) {
-    return element.getName();
-  }
-
-}

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

@@ -33,8 +33,10 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
     List<Element> result = new ArrayList<>();
     for (T sbmlElement : getSbmlElementList(sbmlModel)) {
       Element element = parse(sbmlElement, sbmlModel);
-      result.add(element);
-      elementBySbmlId.put(element.getElementId(), element);
+      if (element != null) {
+        result.add(element);
+        elementBySbmlId.put(element.getElementId(), element);
+      }
     }
     return result;
   }

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

 package lcsb.mapviewer.converter.model.sbml;
 
+import java.io.UnsupportedEncodingException;
+
 import javax.xml.stream.XMLStreamException;
 
 import org.apache.commons.io.output.ByteArrayOutputStream;
@@ -14,6 +16,9 @@ import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
 import org.sbml.jsbml.ext.render.GlobalRenderInformation;
 import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
 
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
 import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
@@ -25,35 +30,40 @@ public class SbmlExporter {
 
   public String toXml(lcsb.mapviewer.model.map.model.Model model)
       throws SBMLException, XMLStreamException, InconsistentModelException {
-    SBMLDocument doc = new SBMLDocument(3, 1);
-    Model result = doc.createModel(model.getIdModel());
-    result.setName(model.getName());
-    Layout layout = createSbmlLayout(model, result);
+    try {
+      SBMLDocument doc = new SBMLDocument(3, 2);
+      Model result = doc.createModel(model.getIdModel());
+      result.setName(model.getName());
+      Layout layout = createSbmlLayout(model, result);
 
-    SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
-    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
-        compartmentExporter);
-    SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
-        compartmentExporter);
-    SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
-    SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
-    SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
+      SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
+      SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+          compartmentExporter);
+      SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
+          compartmentExporter);
+      SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
+      SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
+      SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
 
-    compartmentExporter.exportElements(result);
-    speciesExporter.exportElements(result);
-    reactionExporter.exportElements(result);
-    unitExporter.exportUnits(result);
-    parameterExporter.exportParameter(result);
-    functionExporter.exportFunction(result);
+      compartmentExporter.exportElements(result);
+      speciesExporter.exportElements(result);
+      reactionExporter.exportElements(result);
+      unitExporter.exportUnits(result);
+      parameterExporter.exportParameter(result);
+      functionExporter.exportFunction(result);
 
-    ByteArrayOutputStream stream = new ByteArrayOutputStream();
-    SBMLWriter.write(doc, stream, "minerva", "1.0");
-    return stream.toString();
+      ByteArrayOutputStream stream = new ByteArrayOutputStream();
+      SBMLWriter.write(doc, stream, "minerva", Configuration.getSystemVersion(null));
+      return stream.toString("UTF-8");
+    } catch (UnsupportedEncodingException e) {
+      throw new InvalidStateException(e);
+    }
   }
 
   public Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
     LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(result);
     Layout layout = new Layout();
+    layout.setId("minerva_layout");
     Dimensions dimensions = new Dimensions();
     if (model.getHeight() != null) {
       dimensions.setHeight(model.getHeight());
@@ -68,7 +78,7 @@ public class SbmlExporter {
     layout.setDimensions(dimensions);
     layoutPlugin.add(layout);
     result.addExtension("layout", layoutPlugin);
-    
+
     createSbmlRenderPlugin(layout, result);
     return layout;
   }

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

@@ -29,12 +29,14 @@ import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.IConverter;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
 import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.modifier.Modulation;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java

+package lcsb.mapviewer.converter.model.sbml.compartment;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.BoundingBox;
+import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.Point;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
+  Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
+
+  public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+    super(layout, minervaModel);
+  }
+
+  @Override
+  public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
+    org.sbml.jsbml.Compartment result;
+    if (element == null || element.getElementId().equals("default")) {
+      result = getSbmlModel().createCompartment("default");
+    } else {
+      result = getSbmlModel().createCompartment("comp_" + (getNextId()));
+    }
+    //for now we don't have this information - needed for validation
+    result.setConstant(false);
+    return result;
+  }
+
+  @Override
+  protected List<Compartment> getElementList() {
+    List<Compartment> result = new ArrayList<>();
+    result.addAll(getMinervaModel().getCompartments());
+    boolean defaultFound = false;
+    for (Compartment compartment : result) {
+      if (compartment.getElementId().equals("default")) {
+        defaultFound = true;
+      }
+    }
+    if (!defaultFound) {
+      Compartment defaultCompartment = new Compartment("default");
+      result.add(defaultCompartment);
+    }
+    return result;
+  }
+
+  @Override
+  protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
+    if (sbmlCompartmentId.equals("default")) {
+      glyphId = "default_compartment";
+    }
+    CompartmentGlyph result = getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
+    return result;
+  }
+
+  @Override
+  protected String getSbmlIdKey(Compartment compartment) {
+    if (compartment == null || compartment.getElementId().equals("default")) {
+      return "default";
+    }
+    return compartment.getName();
+  }
+
+  @Override
+  protected void assignLayoutToGlyph(Compartment element, AbstractReferenceGlyph speciesGlyph) {
+    if (element.getElementId().equals("default")) {
+      BoundingBox boundingBox = new BoundingBox();
+
+      boundingBox.setPosition(new Point(element.getX(), element.getY()));
+      Dimensions dimensions = new Dimensions();
+
+      if (getMinervaModel().getWidth() != null) {
+        dimensions.setWidth(getMinervaModel().getWidth());
+        dimensions.setHeight(getMinervaModel().getHeight());
+      }
+      boundingBox.setDimensions(dimensions);
+      speciesGlyph.setBoundingBox(boundingBox);
+    } else {
+      super.assignLayoutToGlyph(element, speciesGlyph);
+    }
+  }
+
+  @Override
+  public org.sbml.jsbml.Compartment getSbmlElement(Compartment element) throws InconsistentModelException {
+    String mapKey = getSbmlIdKey(element);
+    if (element == null && sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
+      org.sbml.jsbml.Compartment sbmlElement = createSbmlElement(element);
+      sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
+    }
+    return super.getSbmlElement(element);
+  }
+
+}

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java → converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java

-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.compartment;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.layout.Layout;
 import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.SbmlElementParser;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.species.Element;
@@ -27,6 +28,9 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
   @Override
   protected Compartment parse(org.sbml.jsbml.Compartment compartment, Model sbmlModel)
       throws InvalidInputDataExecption {
+    if (compartment.getId().equals("default")) {
+      return null;
+    }
     Compartment result = new SquareCompartment(compartment.getId());
     assignBioEntityData(compartment, result);
     return result;
@@ -38,7 +42,7 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
   }
 
   @Override
-  protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
+  public List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
       throws InvalidInputDataExecption {
     List<Element> result = super.mergeLayout(elements, sbmlLayout, sbmlModel);
 
@@ -64,7 +68,9 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
   protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout) {
     List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
     for (CompartmentGlyph glyph : sbmlLayout.getListOfCompartmentGlyphs()) {
-      result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getCompartment(), glyph));
+      if (!glyph.getCompartment().equals("default")) {
+        result.add(new Pair<>(glyph.getCompartment(), glyph));
+      }
     }
     return result;
   }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -77,11 +77,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     for (Product product : reaction.getProducts()) {
       Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
       SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
+      speciesReference.setConstant(false);
       speciesReferenceByReactionNode.put(product, speciesReference);
     }
     for (Reactant reactant : reaction.getReactants()) {
       Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(reactant.getElement().getElementId());
       SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
+      speciesReference.setConstant(false);
       speciesReferenceByReactionNode.put(reactant, speciesReference);
     }
     for (Modifier modifier : reaction.getModifiers()) {
@@ -261,13 +263,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   }
 
   private LocalStyle createStyleForModifier(Modifier modifier) {
-    LocalRenderInformation renderInformation = new LocalRenderInformation();
+    LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
     LocalStyle style = new LocalStyle();
     style.getRoleList()
         .add("style_" + modifier.getReaction().getElementId() + "_modifier_" + modifier.getElement().getElementId());
     style.setGroup(new RenderGroup());
     renderInformation.addLocalStyle(style);
-    getRenderPlugin().addLocalRenderInformation(renderInformation);
     style.getGroup().setStroke(modifier.getLine().getType().name());
     return style;
   }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -35,8 +35,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
 import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentParser;
 import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.ArrowTypeData;

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

@@ -7,8 +7,8 @@ import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.render.LocalStyle;
 
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.species.Species;
 
@@ -26,12 +26,19 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
   public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
     org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
     result.setSBOTerm(SBOTermSpeciesType.getTermByType(element.getClass()));
-    if (element.getCompartment() != null) {
-      result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
-    }
+    result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
     if (element.getInitialAmount() != null) {
       result.setInitialAmount(element.getInitialAmount());
     }
+    if (element.hasOnlySubstanceUnits() != null) {
+      result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
+    }
+    if (element.getBoundaryCondition() != null) {
+      result.setBoundaryCondition(element.getBoundaryCondition());
+    }
+    if (element.getConstant() != null) {
+      result.setConstant(element.getConstant());
+    }
     return result;
   }
 
@@ -56,7 +63,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     if (element.getComplex() != null) {
       complexName = element.getComplex().getName();
     }
-    return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName+ "\n" + complexName;
+    return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName;
   }
 
   protected LocalStyle createStyle(Species element) {

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

@@ -37,6 +37,15 @@ 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());
+      }
+      if (species.isSetBoundaryCondition()) {
+        result.setBoundaryCondition(species.getBoundaryCondition());
+      }
+      if (species.isSetConstant()) {
+        result.setConstant(species.getConstant());
+      }
       assignBioEntityData(species, result);
       if (layout == null) {
         assignCompartment(result, species.getCompartment());
@@ -71,7 +80,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
     if (compartment == null && layout != null) {
       List<Compartment> compartments = new ArrayList<>();
       for (CompartmentGlyph glyph : layout.getListOfCompartmentGlyphs()) {
-        if (glyph.getCompartment().equals(compartmentId)) {
+        if (glyph.getCompartment().equals(compartmentId) && !glyph.getCompartment().equals("default")) {
           compartments.add(minervaModel.getElementByElementId(glyph.getId()));
         }
       }

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

@@ -68,7 +68,6 @@ public class SbmlExporterTest {
 
   private Model getModelAfterSerializing(Model originalModel) throws Exception {
     String xml = exporter.toXml(originalModel);
-    logger.debug(xml);
     ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
     Model result = parser.createModel(new ConverterParams().inputStream(stream));
     // showImage(originalModel);
@@ -184,6 +183,8 @@ public class SbmlExporterTest {
 
   private Model createModelWithReaction() {
     Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
     GenericProtein p1 = new GenericProtein("s1");
     p1.setWidth(100);
     p1.setHeight(20);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java

@@ -68,31 +68,17 @@ public class SbmlReactionExportArrowType {
     Model model = new ModelFullIndexed(null);
     model.setWidth(1000);
     model.setHeight(1000);
-    Ion ion = new Ion("x1");
-    ion.setName("ion 1");
-    ion.setWidth(100);
-    ion.setHeight(100);
-    ion.setX(200);
-    ion.setY(50);
+    Ion ion = createIon(1);
     model.addElement(ion);
 
-    Ion ion2 = new Ion("x2");
-    ion2.setName("ion 1");
-    ion2.setWidth(100);
-    ion2.setHeight(100);
-    ion2.setX(200);
-    ion2.setY(250);
+    Ion ion2 = createIon(2);
     model.addElement(ion2);
 
-    Ion ion3 = new Ion("x3");
-    ion3.setName("ion 1");
-    ion3.setWidth(100);
-    ion3.setHeight(100);
-    ion3.setX(400);
-    ion3.setY(450);
+    Ion ion3 = createIon(3);
     model.addElement(ion3);
 
     Reaction reaction = (Reaction) clazz.getConstructor().newInstance();
+    reaction.setIdReaction("reactionId");
     reaction.addReactant(createReactant(ion));
     Product product = createProduct(ion2);
     reaction.addProduct(product);
@@ -133,6 +119,20 @@ public class SbmlReactionExportArrowType {
     return modelAfterSerialization;
   }
 
+  private static Ion createIon(int id) {
+    Ion ion = new Ion("x" + id);
+    ion.setName("ion " + id);
+    ion.setWidth(100);
+    ion.setHeight(100);
+    ion.setX(200 * (id % 2 + 1));
+    ion.setY(50 * (id / 2 + 1));
+    ion.setOnlySubstanceUnits(true);
+    ion.setConstant(true);
+    ion.setInitialAmount(2.0);
+    ion.setBoundaryCondition(true);
+    return ion;
+  }
+
   private static Reactant createReactant(Ion ion) {
     Reactant result = new Reactant(ion);
     Point2D point = ion.getCenter();
@@ -164,7 +164,7 @@ public class SbmlReactionExportArrowType {
 
       Reaction originalReaction = modelToBeTested.getReactions().iterator().next();
       Reaction afterSerializationReaction = modelAfterSerialization.getReactions().iterator().next();
-      
+
       afterSerializationReaction.setIdReaction(originalReaction.getIdReaction());
       assertEquals(0, reactionComparator.compare(originalReaction, afterSerializationReaction));
     } catch (Exception e) {

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java

@@ -10,7 +10,7 @@ import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
 
 import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;

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

@@ -7,8 +7,8 @@ import org.junit.Test;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.ext.layout.Layout;
 
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;

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>
\ No newline at end of file