From 6904198bf8b6a6f1bb265b7acd9ff0d7ab4f083a Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 27 Jan 2017 11:05:08 +0100
Subject: [PATCH] error handling ehen there is an issue with mesh data
---
.../annotation/cache/XmlSerializer.java | 4 +++-
.../annotation/services/MeSHParser.java | 19 ++++++++++++++-----
2 files changed, 17 insertions(+), 6 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
index 1a9866cae4..1f51982375 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
@@ -20,7 +20,7 @@ import org.w3c.dom.Node;
* type of the object to serialize
*/
public class XmlSerializer<T> {
-
+
/**
* Class of the object that DAO works on.
*/
@@ -93,6 +93,8 @@ public class XmlSerializer<T> {
return (T) jaxbUnmarshaller.unmarshal(node);
} catch (JAXBException e) {
throw new SerializationException(e);
+ } catch (Exception e) { //the library can throw NPE sometimes...
+ throw new SerializationException(e);
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
index dda935775b..125a040e3a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
@@ -2,6 +2,9 @@ package lcsb.mapviewer.annotation.services;
import java.io.IOException;
+import javax.sql.rowset.serial.SerialException;
+
+import org.apache.commons.lang3.SerializationException;
import org.apache.log4j.Logger;
import org.w3c.dom.Node;
@@ -100,16 +103,22 @@ 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 cached info about mesh: " + meshID);
+ mesh = null;
+ }
+ }
+ 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;
--
GitLab