error handling improved in serialization of mesh data

annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java

@@ -53,7 +53,7 @@ public class XmlSerializer<T> {
 			jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
 			jaxbUnmarshaller = jaxbContext.createUnmarshaller();
 		} catch (JAXBException e) {
-			throw new SerializationException();
+			throw new SerializationException(e);
 		}
 	}
 
@@ -73,6 +73,8 @@ public class XmlSerializer<T> {
 			jaxbMarshaller.marshal(object, sw);
 		} catch (JAXBException e) {
 			throw new SerializationException(e);
+		} catch (Exception e) {
+			throw new SerializationException(e);
 		}
 		return sw.toString();
 	}
@@ -93,6 +95,8 @@ public class XmlSerializer<T> {
 			return (T) jaxbUnmarshaller.unmarshal(node);
 		} catch (JAXBException e) {
 			throw new SerializationException(e);
+		} catch (Exception e) {
+			throw new SerializationException(e);
 		}
 	}
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
 
+import org.apache.commons.lang3.SerializationException;
 import org.apache.log4j.Logger;
 import org.w3c.dom.Node;
 
@@ -100,16 +101,21 @@ public class MeSHParser extends CachableInterface implements IExternalService {
 		String id = getIdentifier(meshID);
 		Node meshNode = super.getCacheNode(id);
 		if (meshNode != null && meshNode.hasChildNodes()) {
-			mesh = meshSerializer.xmlToObject(meshNode);
-		} else {
+			try {
+				mesh = meshSerializer.xmlToObject(meshNode);
+			} catch (SerializationException e) {
+				logger.warn("Problem with processing mesh data for: " + meshID);
+			}
+		}
+		if (mesh == null) {
 			try {
 				mesh = getMeSHByIdFromDB(meshID);
 			} catch (IOException e) {
 				throw new AnnotatorException("Problem with accessing MeSH database", e);
 			}
-			if (mesh != null) {
-				super.setCacheValue(id, this.meshSerializer.objectToString(mesh));
-			}
+		}
+		if (mesh != null) {
+			super.setCacheValue(id, this.meshSerializer.objectToString(mesh));
 		}
 
 		return mesh;