with null notes there is fallback to empty string

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

@@ -2,12 +2,13 @@ package lcsb.mapviewer.converter.model.sbml;
 
 import javax.xml.stream.XMLStreamException;
 
+import org.apache.commons.lang3.StringEscapeUtils;
 import org.sbml.jsbml.AbstractNamedSBase;
 
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 
 public class NotesUtility {
-  public static  String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
+  public static String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
     String notes = "";
     try {
       notes = sbmlElement.getNotesString();
@@ -28,5 +29,11 @@ public class NotesUtility {
     return notes;
   }
 
+  public static String prepareEscapedXmlNotes(String notes) {
+    if (notes == null) {
+      return "";
+    }
+    return StringEscapeUtils.escapeXml(notes);
+  }
 
 }

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

@@ -9,7 +9,6 @@ import java.util.Set;
 
 import javax.xml.stream.XMLStreamException;
 
-import org.apache.commons.lang3.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.SBasePlugin;
@@ -116,7 +115,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
       }
       sbmlElement.setName(element.getName());
       try {
-        sbmlElement.setNotes(StringEscapeUtils.escapeXml(element.getNotes()));
+        sbmlElement.setNotes(NotesUtility.prepareEscapedXmlNotes(element.getNotes()));
       } catch (XMLStreamException e) {
         throw new InvalidStateException(e);
       }

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

@@ -9,7 +9,6 @@ import java.util.Set;
 import javax.xml.stream.XMLStreamException;
 
 import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.apache.commons.lang3.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBMLDocument;
@@ -80,7 +79,7 @@ public class SbmlExporter {
     Model result = doc.createModel(model.getIdModel());
     result.setName(model.getName());
     try {
-      result.setNotes(StringEscapeUtils.escapeXml(model.getNotes()));
+      result.setNotes(NotesUtility.prepareEscapedXmlNotes(model.getNotes()));
     } catch (XMLStreamException e) {
       throw new InvalidStateException(e);
     }