From 0e4cbf8f9078c7a04be28c35f9ee857657836d4c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 24 Jul 2017 15:49:49 +0200
Subject: [PATCH] error handling for xml serialization improved to catch all
library errors
---
.../cache/PermanentDatabaseLevelCache.java | 10 ++++++----
.../mapviewer/annotation/cache/XmlSerializer.java | 12 ++++++++----
.../annotation/data/TargettingStructure.java | 15 +++++++++++++++
.../annotation/services/PubmedParser.java | 6 +++++-
4 files changed, 34 insertions(+), 9 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
index 985aa13906..607a26f3ba 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -448,12 +448,14 @@ public class PermanentDatabaseLevelCache extends XmlParser implements PermanentD
try {
Document document = getXmlDocumentFromString(entry.getValue());
Calendar currentDate = Calendar.getInstance();
- if (currentDate.before(entry.getExpires())) {
- return document.getFirstChild();
- } else {
+ if (currentDate.after(entry.getExpires())) {
cacheRefreshService.submit(new RefreshTask(query, type));
- return document.getFirstChild();
}
+ Node result = null;
+ if (document != null) {
+ result = document.getFirstChild();
+ }
+ return result;
} catch (InvalidXmlSchemaException e) {
logger.warn("Invalid xml for query: " + query);
logger.warn("xml: " + entry.getValue());
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 4a5535ec10..37bf7e7338 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
@@ -8,6 +8,7 @@ import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import org.apache.commons.lang3.SerializationException;
+import org.apache.log4j.Logger;
import org.w3c.dom.Node;
/**
@@ -20,7 +21,8 @@ import org.w3c.dom.Node;
* type of the object to serialize
*/
public class XmlSerializer<T> {
-
+ private final Logger logger = Logger.getLogger(XmlSerializer.class);
+
/**
* Class of the object that DAO works on.
*/
@@ -74,7 +76,8 @@ public class XmlSerializer<T> {
} catch (JAXBException e) {
throw new SerializationException(e);
} catch (Exception e) {
- throw new SerializationException(e);
+ logger.error(e, e);
+ return null;
}
return sw.toString();
}
@@ -95,8 +98,9 @@ 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);
+ } catch (Exception e) { // the library can throw NPE sometimes...
+ logger.error(e, e);
+ return null;
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
index 6c704dc1d3..c35645c3da 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
@@ -4,10 +4,25 @@ import java.util.Collection;
import lcsb.mapviewer.model.map.MiriamData;
+/**
+ * Interface for all externall objects that interact with elements on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
public interface TargettingStructure {
+ /**
+ *
+ * @return list of {@link MiriamData annotations} that describe source of this
+ * object
+ */
Collection<MiriamData> getSources();
+ /**
+ *
+ * @return list of {@link Target targets} with which object is interacting
+ */
Collection<Target> getTargets();
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index f676f785ac..851847b75d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -183,7 +183,11 @@ public class PubmedParser extends CachableInterface implements IExternalService
result.setId(id + "");
if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
- setCacheValue(queryString, articleSerializer.objectToString(result));
+ try {
+ setCacheValue(queryString, articleSerializer.objectToString(result));
+ } catch (SerializationException e) {
+ logger.warn("Problem with serialization of the string: " + queryString);
+ }
} else {
result = null;
}
--
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