Merge branch '395-error-when-exporting-reconmap-to-sbml' into 'master'

Resolve "Error when exporting ReconMap to SBML"

Closes #395

See merge request piotr.gawron/minerva!293

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

@@ -6,6 +6,7 @@ import java.util.Map;
 
 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.layout.AbstractReferenceGlyph;
@@ -72,7 +73,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
       }
       sbmlElement.setName(element.getName());
       try {
-        sbmlElement.setNotes(element.getNotes());
+        sbmlElement.setNotes(StringEscapeUtils.escapeXml(element.getNotes()));
       } catch (XMLStreamException e) {
         throw new InvalidStateException(e);
       }

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

@@ -261,4 +261,17 @@ public class SbmlExporterTest {
     assertEquals(0, comparator.compare(model, model2));
 
   }
+  
+  @Test
+  public void testExportProblematicNotes() throws Exception {
+    Model model = createModelWithReaction();
+    Reaction reaction = model.getReactions().iterator().next();
+    reaction.setNotes("X=Y<Z");
+
+    Model deserializedModel = getModelAfterSerializing(model);
+    Reaction deserializedReaction = deserializedModel.getReactions().iterator().next();
+
+    assertEquals(reaction.getNotes(), deserializedReaction.getNotes());
+
+  }
 }