Merge branch '365-the-same-species-appears-multiple-times-in-sbml' into 'master'

Resolve "The same species appears multiple times in SBML"

Closes #365

See merge request piotr.gawron/minerva!265

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

@@ -42,16 +42,16 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     sbmlModel = model;
     Collection<T> speciesList = getElementList();
     for (T species : speciesList) {
-      S sbmlCompartment = getSbmlElement(species, null);
+      S sbmlElement = getSbmlElement(species);
 
       if (sbmlElementByElementId.get(species.getElementId()) != null) {
         throw new InconsistentModelException("More than one species with id: " + species.getElementId());
       }
-      sbmlElementByElementId.put(species.getElementId(), sbmlCompartment);
+      sbmlElementByElementId.put(species.getElementId(), sbmlElement);
     }
     for (T species : speciesList) {
-      AbstractReferenceGlyph compartmentGlyph = createGlyph(species);
-      sbmlGlyphByElementId.put(species.getElementId(), compartmentGlyph);
+      AbstractReferenceGlyph elementGlyph = createGlyph(species);
+      sbmlGlyphByElementId.put(species.getElementId(), elementGlyph);
     }
   }
 
@@ -59,8 +59,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
 
   public abstract S createSbmlElement(T element) throws InconsistentModelException;
 
-  public S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
-    String mapKey = element.getClass().getSimpleName() + "\n" + element.getElementId() + "\n" + compartmentName;
+  public S getSbmlElement(T element) throws InconsistentModelException {
+    String mapKey = getSbmlIdKey(element);
     if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
       S sbmlElement = createSbmlElement(element);
       XmlAnnotationParser parser = new XmlAnnotationParser();
@@ -81,6 +81,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return sbmlElementByElementNameAndCompartmentName.get(mapKey);
   }
 
+  protected abstract String getSbmlIdKey(T element);
+
   protected abstract void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph);
 
   protected AbstractReferenceGlyph createGlyph(T element) {

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

@@ -31,4 +31,9 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
     return getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
   }
 
+  @Override
+  protected String getSbmlIdKey(Compartment element) {
+    return element.getName();
+  }
+
 }

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

@@ -10,6 +10,7 @@ import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.CompartmentGlyph;
 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.model.map.compartment.Compartment;
@@ -44,6 +45,8 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
     for (Element element : result) {
       Compartment parent = element.getCompartment();
       for (Compartment compartment : minervaModel.getCompartments()) {
+        compartment.setNamePoint(compartment.getX() + ApplySimpleLayoutModelCommand.COMPARTMENT_BORDER,
+            compartment.getY() + ApplySimpleLayoutModelCommand.COMPARTMENT_BORDER);
         if (parent == null || parent.getSize() > compartment.getSize()) {
           if (compartment.contains(element)) {
             parent = compartment;

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

@@ -231,4 +231,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     super.setSbmlModel(sbmlModel);
   }
 
+  @Override
+  protected String getSbmlIdKey(Reaction element) {
+    return element.getClass().getSimpleName() + "\n" + element.getElementId();
+  }
+
 }

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

@@ -26,7 +26,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     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(), null));
+      result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
     }
     return result;
   }
@@ -42,4 +42,13 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     return getMinervaModel().getSpeciesList();
   }
 
+  @Override
+  protected String getSbmlIdKey(Species element) {
+    String compartmentName = null;
+    if (element.getCompartment() != null) {
+      compartmentName = element.getCompartment().getName();
+    }
+    return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName;
+  }
+
 }

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

@@ -5,16 +5,16 @@ import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
 import lcsb.mapviewer.converter.model.sbml.reaction.AllSbmlReactionParserTests;
-import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
+import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({ AllSbmlReactionParserTests.class, //
+    AllSbmlSpeciesTests.class, //
     GenericSbmlParserTest.class, //
     GenericSbmlToXmlParserTest.class, //
     SbmlExporterTest.class, //
     SbmlPareserForInvalidReactionTest.class, //
     SbmlParserTest.class, //
-    SbmlSpeciesParserTest.class,//
 })
 public class AllSbmlConverterTests {
 

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

@@ -9,8 +9,11 @@ import java.awt.Desktop;
 import java.awt.geom.Point2D;
 import java.io.ByteArrayInputStream;
 import java.io.File;
+import java.io.InputStream;
+import java.io.StringWriter;
 import java.nio.file.Files;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 import org.junit.Test;
 
@@ -20,6 +23,7 @@ import lcsb.mapviewer.converter.IConverter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
 import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -237,7 +241,7 @@ public class SbmlExporterTest {
     assertEquals(0, comparator.compare(model, model2));
 
   }
-  
+
   @Test
   public void testExportModelName() throws Exception {
     IConverter converter = new SbmlParser();
@@ -257,7 +261,4 @@ public class SbmlExporterTest {
     assertEquals(0, comparator.compare(model, model2));
 
   }
-  
-  
-
 }

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

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SbmlSpeciesExporterTest.class, SbmlSpeciesParserTest.class })
+public class AllSbmlSpeciesTests {
+
+}

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

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+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.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class SbmlSpeciesExporterTest {
+
+  Logger logger = Logger.getLogger(SbmlSpeciesExporterTest.class);
+
+  SbmlCompartmentExporter compartmentExporter;
+
+  org.sbml.jsbml.Model sbmlModel;
+  Layout sbmlLayout;
+
+  @Test
+  public void testOneElementWithTwoAliases() throws InconsistentModelException {
+    Element protein1 = new GenericProtein("sa1");
+    protein1.setName("SNCA");
+    Element protein2 = new GenericProtein("sa2");
+    protein2.setName("SNCA");
+    Model model = new ModelFullIndexed(null);
+    model.addElement(protein1);
+    model.addElement(protein2);
+
+    SbmlSpeciesExporter exporter = createExporter(model);
+
+    exporter.exportElements(sbmlModel);
+
+    assertEquals(1, sbmlModel.getSpeciesCount());
+  }
+
+  @Test
+  public void testOneElementButInTwoCompartments() throws InconsistentModelException {
+    Compartment compartment = new Compartment("c1");
+    compartment.setName("test");
+    Element protein1 = new GenericProtein("sa1");
+    protein1.setName("SNCA");
+    Element protein2 = new GenericProtein("sa2");
+    protein2.setName("SNCA");
+    protein2.setCompartment(compartment);
+    
+    Model model = new ModelFullIndexed(null);
+    model.addElement(protein1);
+    model.addElement(protein2);
+    model.addElement(compartment);
+
+    SbmlSpeciesExporter exporter = createExporter(model);
+
+    exporter.exportElements(sbmlModel);
+
+    assertEquals(2, sbmlModel.getSpeciesCount());
+  }
+
+  private SbmlSpeciesExporter createExporter(Model model) throws InconsistentModelException {
+    SBMLDocument doc = new SBMLDocument(3, 1);
+    sbmlModel = doc.createModel(model.getIdModel());
+
+    LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(sbmlModel);
+    sbmlLayout = new Layout();
+    layoutPlugin.add(sbmlLayout);
+    sbmlModel.addExtension("layout", layoutPlugin);
+
+    SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlLayout, model);
+    compartmentExporter.exportElements(sbmlModel);
+    SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlLayout, model, compartmentExporter);
+    return result;
+  }
+
+}

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -41,7 +41,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
   @SuppressWarnings("unused")
   private Logger logger = Logger.getLogger(ApplySimpleLayoutModelCommand.class);
 
-  private static final double COMPARTMENT_BORDER = 10;
+  public static final double COMPARTMENT_BORDER = 10;
   private static final double BORDER_FROM_EXISTING_ELEMENTS = 10;
   private static final int SPECIES_WIDTH = 90;
   private static final int SPECIES_HEIGHT = 30;