notes are extracted properly

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

@@ -5,6 +5,7 @@ import java.util.Set;
 
 import javax.xml.stream.XMLStreamException;
 
+import org.apache.log4j.Logger;
 import org.sbml.jsbml.AbstractNamedSBase;
 import org.sbml.jsbml.Annotation;
 import org.sbml.jsbml.ext.layout.Layout;
@@ -15,6 +16,7 @@ import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 
 public class SbmlBioEntityParser {
+  Logger logger = Logger.getLogger(SbmlBioEntityParser.class);
 
   protected Layout layout;
   protected lcsb.mapviewer.model.map.model.Model minervaModel;
@@ -31,17 +33,36 @@ public class SbmlBioEntityParser {
     return result;
   }
 
-  protected void assignBioEntityData(AbstractNamedSBase sbmlElement, BioEntity result) throws InvalidInputDataExecption {
+  protected void assignBioEntityData(AbstractNamedSBase sbmlElement, BioEntity result)
+      throws InvalidInputDataExecption {
     result.addMiriamData(parseAnnotation(sbmlElement.getAnnotation()));
     result.setName(sbmlElement.getName());
     if (result.getName() == null || result.getName().isEmpty()) {
       result.setName(result.getElementId());
     }
+    String notes = extractNotes(sbmlElement);
+    result.setNotes(notes);
+  }
+
+  private String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
+    String notes = "";
     try {
-      result.setNotes(sbmlElement.getNotesString());
+      notes = sbmlElement.getNotesString();
     } catch (XMLStreamException e) {
       throw new InvalidInputDataExecption(sbmlElement.getId() + " Invalid notes", e);
     }
+    if (sbmlElement.getNotes() != null) {
+      if (sbmlElement.getNotes().getChildCount() > 1) {
+        if (sbmlElement.getNotes().getChild(1).getChildCount() > 1) {
+          if (sbmlElement.getNotes().getChild(1).getChild(1).getChildCount() > 0) {
+            notes = sbmlElement.getNotes().getChild(1).getChild(1).getChild(0).getCharacters();
+          } else {
+            notes = sbmlElement.getNotes().getChild(1).getChild(1).getCharacters();
+          }
+        }
+      }
+    }
+    return notes;
   }
 
 }
\ No newline at end of file

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

@@ -5,8 +5,6 @@ import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.xml.stream.XMLStreamException;
-
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.SimpleSpeciesReference;
 import org.sbml.jsbml.Species;
@@ -20,7 +18,6 @@ import org.sbml.jsbml.ext.layout.ReactionGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
 
-import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.modifier.Inhibition;
 import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -43,28 +40,23 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
 
   @Override
   public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
-    try {
-      org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
-      result.setNotes(reaction.getNotes());
-      for (Product product : reaction.getProducts()) {
-        Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
-        SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
-        speciesReferenceByReactionNode.put(product, speciesReference);
-      }
-      for (Reactant reactant : reaction.getReactants()) {
-        Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
-        SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
-        speciesReferenceByReactionNode.put(reactant, speciesReference);
-      }
-      for (Modifier modifier : reaction.getModifiers()) {
-        Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
-        SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
-        speciesReferenceByReactionNode.put(modifier, speciesReference);
-      }
-      return result;
-    } catch (XMLStreamException e) {
-      throw new InvalidStateException(e);
+    org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
+    for (Product product : reaction.getProducts()) {
+      Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
+      SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
+      speciesReferenceByReactionNode.put(product, speciesReference);
+    }
+    for (Reactant reactant : reaction.getReactants()) {
+      Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
+      SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
+      speciesReferenceByReactionNode.put(reactant, speciesReference);
+    }
+    for (Modifier modifier : reaction.getModifiers()) {
+      Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
+      SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
+      speciesReferenceByReactionNode.put(modifier, speciesReference);
     }
+    return result;
   }
 
   @Override