when exporting custom properties strings are properly escaped as xml parameters

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -160,8 +160,9 @@ public class RestAnnotationParser extends XmlParser {
         return "";
       }
     } else if (value instanceof String) {
-      if (!((String) value).trim().isEmpty() || forceFullInfo) {
-        return type.getCommonName() + ": " + value + "\n";
+      String string =(String) value; 
+      if (!(string.trim().isEmpty()) || forceFullInfo) {
+        return type.getCommonName() + ": " + super.escapeXml(string) + "\n";
       } else {
         return "";
       }
@@ -178,7 +179,7 @@ public class RestAnnotationParser extends XmlParser {
           if (object instanceof MiriamData) {
             result += ((MiriamData) object).getResource();
           } else {
-            result += object;
+            result += super.escapeXml(object.toString());
           }
 
         }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -54,6 +54,8 @@ import lcsb.mapviewer.model.map.species.Species;
 public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
   Logger logger = Logger.getLogger(CellDesignerXmlParserTest.class);
 
+  ModelComparator modelComparator = new ModelComparator();
+
   @Before
   public void setUp() throws Exception {
   }
@@ -422,8 +424,6 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       InputStream is = new ByteArrayInputStream(xmlString.getBytes());
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
-      ModelComparator modelComparator = new ModelComparator();
-
       assertEquals(0, modelComparator.compare(model, model2));
 
     } catch (Exception e) {
@@ -1012,6 +1012,34 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testSpeciesWithSpecialSynonym() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      model.setIdModel("as");
+      model.setWidth(10);
+      model.setHeight(10);
+      Species protein = new GenericProtein("id1");
+      protein.setWidth(10);
+      protein.setHeight(10);
+      protein.setName("ROS");
+      protein.addSynonym("&");
+      model.addElement(protein);
+
+      CellDesignerXmlParser parser = new CellDesignerXmlParser();
+      String xmlString = parser.toXml(model);
+      InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+      Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+      
+      assertEquals(0, modelComparator.compare(model, model2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testReactionCoordsEqual() throws Exception {
     try {